diff --git a/patches/pyink.patch b/patches/pyink.patch
index 0cb94c99c6f..ee82bed7e7a 100644
--- a/patches/pyink.patch
+++ b/patches/pyink.patch
@@ -370,6 +370,19 @@
      )
  
      lines: List[Tuple[int, int]] = []
+@@ -1153,9 +677,10 @@
+     """
+     if any(transformed_magic in src for transformed_magic in TRANSFORMED_MAGICS):
+         raise NothingChanged
++    line = ink.get_code_start(src)
+     if (
+-        src[:2] == "%%"
+-        and src.split()[0][2:] not in PYTHON_CELL_MAGICS | mode.python_cell_magics
++        line[:2] == "%%"
++        and line.split()[0][2:] not in PYTHON_CELL_MAGICS | mode.python_cell_magics
+     ):
+         raise NothingChanged
+ 
 @@ -1175,7 +1219,6 @@
          raise NothingChanged
  
@@ -1395,6 +1408,19 @@
  
  runner = CliRunner()
  
+@@ -209,6 +209,12 @@
+         assert result == expected_output
+ 
+ 
++def test_cell_magic_with_custom_python_magic_after_spaces_and_comments_noop() -> None:
++    src = "\n  \n # comment\n\t\n %%custom_python_magic \nx=2"
++    with pytest.raises(NothingChanged):
++        format_cell(src, fast=True, mode=JUPYTER_MODE)
++
++
+ def test_cell_magic_nested() -> None:
+     src = "%%time\n%%time\n2+2"
+     result = format_cell(src, fast=True, mode=JUPYTER_MODE)
 @@ -385,6 +385,45 @@
      assert result == expected
  
diff --git a/src/pyink/__init__.py b/src/pyink/__init__.py
index f96ac01cb20..2d160691a2f 100644
--- a/src/pyink/__init__.py
+++ b/src/pyink/__init__.py
@@ -1150,9 +1150,10 @@ def validate_cell(src: str, mode: Mode) -> None:
     """
     if any(transformed_magic in src for transformed_magic in TRANSFORMED_MAGICS):
         raise NothingChanged
+    line = ink.get_code_start(src)
     if (
-        src[:2] == "%%"
-        and src.split()[0][2:] not in PYTHON_CELL_MAGICS | mode.python_cell_magics
+        line[:2] == "%%"
+        and line.split()[0][2:] not in PYTHON_CELL_MAGICS | mode.python_cell_magics
     ):
         raise NothingChanged
 
diff --git a/src/pyink/ink.py b/src/pyink/ink.py
index 6cd4b3ffdd1..2cb219972e6 100644
--- a/src/pyink/ink.py
+++ b/src/pyink/ink.py
@@ -3,6 +3,7 @@
 This is a separate module for easier patch management.
 """
 
+import re
 from typing import (
     Collection,
     Iterator,
@@ -62,6 +63,26 @@ def majority_quote(node: LN) -> Quote:
     return Quote.DOUBLE
 
 
+def get_code_start(src: str) -> str:
+    """Provides the first line where the code starts.
+
+    Iterates over lines of code until it finds the first line that doesn't
+    contain only empty spaces and comments. If such line doesn't exist, it
+    returns an empty string.
+
+    Args:
+      src: The multi-line source code.
+
+    Returns:
+      The first line of code without initial spaces or an empty string.
+    """
+    for match in re.finditer(".+", src):
+        line = match.group(0).lstrip()
+        if line and not line.startswith("#"):
+            return line
+    return ""
+
+
 def convert_unchanged_lines(src_node: Node, lines: Collection[Tuple[int, int]]):
     """Converts unchanged lines to STANDALONE_COMMENT.
 
diff --git a/tests/test_ipynb.py b/tests/test_ipynb.py
index 7cd2950eb82..115cea65d97 100644
--- a/tests/test_ipynb.py
+++ b/tests/test_ipynb.py
@@ -210,6 +210,12 @@ def test_cell_magic_with_custom_python_magic(
         assert result == expected_output
 
 
+def test_cell_magic_with_custom_python_magic_after_spaces_and_comments_noop() -> None:
+    src = "\n  \n # comment\n\t\n %%custom_python_magic \nx=2"
+    with pytest.raises(NothingChanged):
+        format_cell(src, fast=True, mode=JUPYTER_MODE)
+
+
 def test_cell_magic_nested() -> None:
     src = "%%time\n%%time\n2+2"
     result = format_cell(src, fast=True, mode=JUPYTER_MODE)