diff --git a/native/shuffle/src/partitioners/empty_schema.rs b/native/shuffle/src/partitioners/empty_schema.rs
new file mode 100644
index 0000000000..45decfec05
--- /dev/null
+++ b/native/shuffle/src/partitioners/empty_schema.rs
@@ -0,0 +1,135 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this file
+// to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.  You may obtain a copy of the License at
+//
+//   http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing,
+// software distributed under the License is distributed on an
+// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+// KIND, either express or implied.  See the License for the
+// specific language governing permissions and limitations
+// under the License.
+
+use crate::metrics::ShufflePartitionerMetrics;
+use crate::partitioners::ShufflePartitioner;
+use crate::ShuffleBlockWriter;
+use arrow::array::RecordBatch;
+use arrow::datatypes::SchemaRef;
+use datafusion::common::DataFusionError;
+use std::fs::OpenOptions;
+use std::io::{BufWriter, Seek, Write};
+use tokio::time::Instant;
+
+/// A partitioner for zero-column schemas (e.g. queries where ColumnPruning removes all columns).
+/// This handles shuffles for operations like COUNT(*) that produce empty-schema record batches
+/// but contain a valid row count. Accumulates the total row count and writes a single
+/// zero-column IPC batch to partition 0. All other partitions get empty entries in the index file.
+pub(crate) struct EmptySchemaShufflePartitioner {
+    output_data_file: String,
+    output_index_file: String,
+    schema: SchemaRef,
+    shuffle_block_writer: ShuffleBlockWriter,
+    num_output_partitions: usize,
+    total_rows: usize,
+    metrics: ShufflePartitionerMetrics,
+}
+
+impl EmptySchemaShufflePartitioner {
+    pub(crate) fn try_new(
+        output_data_file: String,
+        output_index_file: String,
+        schema: SchemaRef,
+        num_output_partitions: usize,
+        metrics: ShufflePartitionerMetrics,
+        codec: crate::CompressionCodec,
+    ) -> datafusion::common::Result<Self> {
+        debug_assert!(
+            schema.fields().is_empty(),
+            "EmptySchemaShufflePartitioner requires a zero-column schema"
+        );
+        let shuffle_block_writer = ShuffleBlockWriter::try_new(schema.as_ref(), codec)?;
+        Ok(Self {
+            output_data_file,
+            output_index_file,
+            schema,
+            shuffle_block_writer,
+            num_output_partitions,
+            total_rows: 0,
+            metrics,
+        })
+    }
+}
+
+#[async_trait::async_trait]
+impl ShufflePartitioner for EmptySchemaShufflePartitioner {
+    async fn insert_batch(&mut self, batch: RecordBatch) -> datafusion::common::Result<()> {
+        let start_time = Instant::now();
+        let num_rows = batch.num_rows();
+        if num_rows > 0 {
+            self.total_rows += num_rows;
+            self.metrics.baseline.record_output(num_rows);
+        }
+        self.metrics.input_batches.add(1);
+        self.metrics
+            .baseline
+            .elapsed_compute()
+            .add_duration(start_time.elapsed());
+        Ok(())
+    }
+
+    fn shuffle_write(&mut self) -> datafusion::common::Result<()> {
+        let start_time = Instant::now();
+
+        let output_data = OpenOptions::new()
+            .write(true)
+            .create(true)
+            .truncate(true)
+            .open(&self.output_data_file)
+            .map_err(|e| DataFusionError::Execution(format!("shuffle write error: {e:?}")))?;
+        let mut output_data = BufWriter::new(output_data);
+
+        // Write a single zero-column batch with the accumulated row count to partition 0
+        if self.total_rows > 0 {
+            let batch = RecordBatch::try_new_with_options(
+                self.schema.clone(),
+                vec![],
+                &arrow::array::RecordBatchOptions::new().with_row_count(Some(self.total_rows)),
+            )?;
+            self.shuffle_block_writer.write_batch(
+                &batch,
+                &mut output_data,
+                &self.metrics.encode_time,
+            )?;
+        }
+
+        let mut write_timer = self.metrics.write_time.timer();
+        output_data.flush()?;
+        let data_file_length = output_data.stream_position()?;
+
+        // Write index file: partition 0 spans [0, data_file_length), all others are empty
+        let index_file = OpenOptions::new()
+            .write(true)
+            .create(true)
+            .truncate(true)
+            .open(&self.output_index_file)
+            .map_err(|e| DataFusionError::Execution(format!("shuffle write error: {e:?}")))?;
+        let mut index_writer = BufWriter::new(index_file);
+        index_writer.write_all(&0i64.to_le_bytes())?;
+        for _ in 0..self.num_output_partitions {
+            index_writer.write_all(&(data_file_length as i64).to_le_bytes())?;
+        }
+        index_writer.flush()?;
+        write_timer.stop();
+
+        self.metrics
+            .baseline
+            .elapsed_compute()
+            .add_duration(start_time.elapsed());
+        Ok(())
+    }
+}
diff --git a/native/shuffle/src/partitioners/mod.rs b/native/shuffle/src/partitioners/mod.rs
index 3eedef62c7..a0bc652b4b 100644
--- a/native/shuffle/src/partitioners/mod.rs
+++ b/native/shuffle/src/partitioners/mod.rs
@@ -15,11 +15,13 @@
 // specific language governing permissions and limitations
 // under the License.
 
+mod empty_schema;
 mod multi_partition;
 mod partitioned_batch_iterator;
 mod single_partition;
 mod traits;
 
+pub(crate) use empty_schema::EmptySchemaShufflePartitioner;
 pub(crate) use multi_partition::MultiPartitionShuffleRepartitioner;
 pub(crate) use partitioned_batch_iterator::PartitionedBatchIterator;
 pub(crate) use single_partition::SinglePartitionShufflePartitioner;
diff --git a/native/shuffle/src/shuffle_writer.rs b/native/shuffle/src/shuffle_writer.rs
index e649aaac69..837d3b72f3 100644
--- a/native/shuffle/src/shuffle_writer.rs
+++ b/native/shuffle/src/shuffle_writer.rs
@@ -19,7 +19,8 @@
 
 use crate::metrics::ShufflePartitionerMetrics;
 use crate::partitioners::{
-    MultiPartitionShuffleRepartitioner, ShufflePartitioner, SinglePartitionShufflePartitioner,
+    EmptySchemaShufflePartitioner, MultiPartitionShuffleRepartitioner, ShufflePartitioner,
+    SinglePartitionShufflePartitioner,
 };
 use crate::{CometPartitioning, CompressionCodec};
 use async_trait::async_trait;
@@ -215,6 +216,17 @@ async fn external_shuffle(
         let schema = input.schema();
 
         let mut repartitioner: Box<dyn ShufflePartitioner> = match &partitioning {
+            _ if schema.fields().is_empty() => {
+                log::debug!("found empty schema, overriding {partitioning:?} partitioning with EmptySchemaShufflePartitioner");
+                Box::new(EmptySchemaShufflePartitioner::try_new(
+                    output_data_file,
+                    output_index_file,
+                    Arc::clone(&schema),
+                    partitioning.partition_count(),
+                    metrics,
+                    codec,
+                )?)
+            }
             any if any.partition_count() == 1 => {
                 Box::new(SinglePartitionShufflePartitioner::try_new(
                     output_data_file,
@@ -693,4 +705,160 @@ mod test {
         }
         total_rows
     }
+
+    #[test]
+    #[cfg_attr(miri, ignore)]
+    fn test_empty_schema_shuffle_writer() {
+        use std::fs;
+        use std::io::Read;
+
+        let num_rows = 1000;
+        let num_batches = 5;
+        let num_partitions = 10;
+
+        let schema = Arc::new(Schema::new(Vec::<Field>::new()));
+        let batch = RecordBatch::try_new_with_options(
+            Arc::clone(&schema),
+            vec![],
+            &arrow::array::RecordBatchOptions::new().with_row_count(Some(num_rows)),
+        )
+        .unwrap();
+
+        let batches = (0..num_batches).map(|_| batch.clone()).collect::<Vec<_>>();
+        let partitions = &[batches];
+
+        let dir = tempfile::tempdir().unwrap();
+        let data_file = dir.path().join("data.out");
+        let index_file = dir.path().join("index.out");
+
+        let exec = ShuffleWriterExec::try_new(
+            Arc::new(DataSourceExec::new(Arc::new(
+                MemorySourceConfig::try_new(partitions, Arc::clone(&schema), None).unwrap(),
+            ))),
+            CometPartitioning::RoundRobin(num_partitions, 0),
+            CompressionCodec::Zstd(1),
+            data_file.to_str().unwrap().to_string(),
+            index_file.to_str().unwrap().to_string(),
+            false,
+            1024 * 1024,
+        )
+        .unwrap();
+
+        let config = SessionConfig::new();
+        let runtime_env = Arc::new(RuntimeEnvBuilder::new().build().unwrap());
+        let ctx = SessionContext::new_with_config_rt(config, runtime_env);
+        let task_ctx = ctx.task_ctx();
+        let stream = exec.execute(0, task_ctx).unwrap();
+        let rt = Runtime::new().unwrap();
+        rt.block_on(collect(stream)).unwrap();
+
+        // Verify data file is non-empty (contains IPC batch with row count)
+        let mut data = Vec::new();
+        fs::File::open(&data_file)
+            .unwrap()
+            .read_to_end(&mut data)
+            .unwrap();
+        assert!(!data.is_empty(), "Data file should contain IPC data");
+
+        // Verify row count survives roundtrip
+        let total_rows = read_all_ipc_blocks(&data);
+        assert_eq!(
+            total_rows,
+            num_rows * num_batches,
+            "Row count should survive roundtrip"
+        );
+
+        // Verify index file structure: num_partitions + 1 offsets
+        let mut index_data = Vec::new();
+        fs::File::open(&index_file)
+            .unwrap()
+            .read_to_end(&mut index_data)
+            .unwrap();
+        let expected_index_size = (num_partitions + 1) * 8;
+        assert_eq!(index_data.len(), expected_index_size);
+
+        // First offset should be 0
+        let first_offset = i64::from_le_bytes(index_data[0..8].try_into().unwrap());
+        assert_eq!(first_offset, 0);
+
+        // Second offset should equal data file length (partition 0 holds all data)
+        let data_len = data.len() as i64;
+        let second_offset = i64::from_le_bytes(index_data[8..16].try_into().unwrap());
+        assert_eq!(second_offset, data_len);
+
+        // All remaining offsets should equal data file length (empty partitions)
+        for i in 2..=num_partitions {
+            let offset = i64::from_le_bytes(index_data[i * 8..(i + 1) * 8].try_into().unwrap());
+            assert_eq!(
+                offset, data_len,
+                "Partition {i} offset should equal data length"
+            );
+        }
+    }
+
+    #[test]
+    #[cfg_attr(miri, ignore)]
+    fn test_empty_schema_shuffle_writer_zero_rows() {
+        use std::fs;
+        use std::io::Read;
+
+        let num_partitions = 4;
+
+        let schema = Arc::new(Schema::new(Vec::<Field>::new()));
+        let batch = RecordBatch::try_new_with_options(
+            Arc::clone(&schema),
+            vec![],
+            &arrow::array::RecordBatchOptions::new().with_row_count(Some(0)),
+        )
+        .unwrap();
+
+        let batches = vec![batch];
+        let partitions = &[batches];
+
+        let dir = tempfile::tempdir().unwrap();
+        let data_file = dir.path().join("data.out");
+        let index_file = dir.path().join("index.out");
+
+        let exec = ShuffleWriterExec::try_new(
+            Arc::new(DataSourceExec::new(Arc::new(
+                MemorySourceConfig::try_new(partitions, Arc::clone(&schema), None).unwrap(),
+            ))),
+            CometPartitioning::RoundRobin(num_partitions, 0),
+            CompressionCodec::Zstd(1),
+            data_file.to_str().unwrap().to_string(),
+            index_file.to_str().unwrap().to_string(),
+            false,
+            1024 * 1024,
+        )
+        .unwrap();
+
+        let config = SessionConfig::new();
+        let runtime_env = Arc::new(RuntimeEnvBuilder::new().build().unwrap());
+        let ctx = SessionContext::new_with_config_rt(config, runtime_env);
+        let task_ctx = ctx.task_ctx();
+        let stream = exec.execute(0, task_ctx).unwrap();
+        let rt = Runtime::new().unwrap();
+        rt.block_on(collect(stream)).unwrap();
+
+        // Data file should be empty (no rows to write)
+        let mut data = Vec::new();
+        fs::File::open(&data_file)
+            .unwrap()
+            .read_to_end(&mut data)
+            .unwrap();
+        assert!(data.is_empty(), "Data file should be empty with zero rows");
+
+        // Index file should have all-zero offsets
+        let mut index_data = Vec::new();
+        fs::File::open(&index_file)
+            .unwrap()
+            .read_to_end(&mut index_data)
+            .unwrap();
+        let expected_index_size = (num_partitions + 1) * 8;
+        assert_eq!(index_data.len(), expected_index_size);
+        for i in 0..=num_partitions {
+            let offset = i64::from_le_bytes(index_data[i * 8..(i + 1) * 8].try_into().unwrap());
+            assert_eq!(offset, 0, "All offsets should be 0 with zero rows");
+        }
+    }
 }
diff --git a/spark/src/test/scala/org/apache/comet/exec/CometNativeShuffleSuite.scala b/spark/src/test/scala/org/apache/comet/exec/CometNativeShuffleSuite.scala
index ee29710ee2..751bf4c1f5 100644
--- a/spark/src/test/scala/org/apache/comet/exec/CometNativeShuffleSuite.scala
+++ b/spark/src/test/scala/org/apache/comet/exec/CometNativeShuffleSuite.scala
@@ -468,4 +468,35 @@ class CometNativeShuffleSuite extends CometTestBase with AdaptiveSparkPlanHelper
       }
     }
   }
+
+  // Regression test for https://github.com/apache/datafusion-comet/issues/3846
+  test("repartition count") {
+    withTempPath { dir =>
+      withSQLConf(CometConf.COMET_ENABLED.key -> "false") {
+        spark
+          .range(1000)
+          .selectExpr("id", "concat('name_', id) as name")
+          .repartition(100)
+          .write
+          .parquet(dir.toString)
+      }
+      withSQLConf(
+        CometConf.COMET_NATIVE_SCAN_IMPL.key -> CometConf.SCAN_NATIVE_DATAFUSION,
+        CometConf.COMET_EXEC_SHUFFLE_WITH_ROUND_ROBIN_PARTITIONING_ENABLED.key -> "true") {
+        val testDF = spark.read.parquet(dir.toString).repartition(10)
+        // Verify CometShuffleExchangeExec is in the plan
+        assert(
+          find(testDF.queryExecution.executedPlan) {
+            case _: CometShuffleExchangeExec => true
+            case _ => false
+          }.isDefined,
+          "Expected CometShuffleExchangeExec in the plan")
+        // Actual validation, no crash
+        val count = testDF.count()
+        assert(count == 1000)
+        // Ensure test df evaluated by Comet
+        checkSparkAnswerAndOperator(testDF)
+      }
+    }
+  }
 }