diff --git a/include/LightGBM/arrow.h b/include/LightGBM/arrow.h
index 3d1c74713bd3..75511e17e72a 100644
--- a/include/LightGBM/arrow.h
+++ b/include/LightGBM/arrow.h
@@ -117,6 +117,7 @@ class ArrowChunkedArray {
                            const struct ArrowSchema* schema) {
     chunks_.reserve(n_chunks);
     for (auto k = 0; k < n_chunks; ++k) {
+      if (chunks[k].length == 0) continue;
       chunks_.push_back(&chunks[k]);
     }
     schema_ = schema;
@@ -220,6 +221,7 @@ class ArrowTable {
       std::vector<const ArrowArray*> children_chunks;
       children_chunks.reserve(n_chunks);
       for (int64_t k = 0; k < n_chunks; ++k) {
+        if (chunks[k].length == 0) continue;
         children_chunks.push_back(chunks[k].children[j]);
       }
       columns_.emplace_back(children_chunks, schema->children[j]);
diff --git a/tests/python_package_test/test_arrow.py b/tests/python_package_test/test_arrow.py
index 5e09465e34b3..7542368dcd63 100644
--- a/tests/python_package_test/test_arrow.py
+++ b/tests/python_package_test/test_arrow.py
@@ -30,18 +30,19 @@
 ]
 
 
-def generate_simple_arrow_table() -> pa.Table:
+def generate_simple_arrow_table(empty_chunks: bool = False) -> pa.Table:
+    c: list[list[int]] = [[]] if empty_chunks else []
     columns = [
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.uint8()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.int8()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.uint16()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.int16()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.uint32()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.int32()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.uint64()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.int64()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.float32()),
-        pa.chunked_array([[1, 2, 3, 4, 5]], type=pa.float64()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.uint8()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.int8()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.uint16()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.int16()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.uint32()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.int32()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.uint64()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.int64()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.float32()),
+        pa.chunked_array(c + [[1, 2, 3]] + c + [[4, 5]] + c, type=pa.float64()),
     ]
     return pa.Table.from_arrays(columns, names=[f"col_{i}" for i in range(len(columns))])
 
@@ -104,6 +105,7 @@ def dummy_dataset_params() -> Dict[str, Any]:
     ("arrow_table_fn", "dataset_params"),
     [  # Use lambda functions here to minimize memory consumption
         (lambda: generate_simple_arrow_table(), dummy_dataset_params()),
+        (lambda: generate_simple_arrow_table(empty_chunks=True), dummy_dataset_params()),
         (lambda: generate_dummy_arrow_table(), dummy_dataset_params()),
         (lambda: generate_nullable_arrow_table(), dummy_dataset_params()),
         (lambda: generate_random_arrow_table(3, 1000, 42), {}),
@@ -160,7 +162,12 @@ def test_dataset_construct_fields_fuzzy():
 
 @pytest.mark.parametrize(
     ["array_type", "label_data"],
-    [(pa.array, [0, 1, 0, 0, 1]), (pa.chunked_array, [[0], [1, 0, 0, 1]])],
+    [
+        (pa.array, [0, 1, 0, 0, 1]),
+        (pa.chunked_array, [[0], [1, 0, 0, 1]]),
+        (pa.chunked_array, [[], [0], [1, 0, 0, 1]]),
+        (pa.chunked_array, [[0], [], [1, 0], [], [], [0, 1], []]),
+    ],
 )
 @pytest.mark.parametrize("arrow_type", _INTEGER_TYPES + _FLOAT_TYPES)
 def test_dataset_construct_labels(array_type, label_data, arrow_type):
@@ -187,7 +194,12 @@ def test_dataset_construct_weights_none():
 
 @pytest.mark.parametrize(
     ["array_type", "weight_data"],
-    [(pa.array, [3, 0.7, 1.5, 0.5, 0.1]), (pa.chunked_array, [[3], [0.7, 1.5, 0.5, 0.1]])],
+    [
+        (pa.array, [3, 0.7, 1.5, 0.5, 0.1]),
+        (pa.chunked_array, [[3], [0.7, 1.5, 0.5, 0.1]]),
+        (pa.chunked_array, [[], [3], [0.7, 1.5, 0.5, 0.1]]),
+        (pa.chunked_array, [[3], [0.7], [], [], [1.5, 0.5, 0.1], []]),
+    ],
 )
 @pytest.mark.parametrize("arrow_type", _FLOAT_TYPES)
 def test_dataset_construct_weights(array_type, weight_data, arrow_type):