diff --git a/IPython/core/inputtransformer2.py b/IPython/core/inputtransformer2.py
index 5285644..7c173c7 100644
--- a/IPython/core/inputtransformer2.py
+++ b/IPython/core/inputtransformer2.py
@@ -94,7 +94,7 @@ def cell_magic(lines):
     if re.match(r'%%\w+\?', lines[0]):
         # This case will be handled by help_end
         return lines
-    magic_name, _, first_line = lines[0][2:-1].partition(' ')
+    magic_name, _, first_line = lines[0][2:].rstrip().partition(' ')
     body = ''.join(lines[1:])
     return ['get_ipython().run_cell_magic(%r, %r, %r)\n'
             % (magic_name, first_line, body)]
@@ -152,8 +152,8 @@ def assemble_continued_line(lines, start: Tuple[int, int], end_line: int):
     multiple lines.
     """
     parts = [lines[start[0]][start[1]:]] + lines[start[0]+1:end_line+1]
-    return ' '.join([p[:-2] for p in parts[:-1]]  # Strip backslash+newline
-                    + [parts[-1][:-1]])         # Strip newline from last line
+    return ' '.join([p.rstrip()[:-1] for p in parts[:-1]]  # Strip backslash+newline
+                    + [parts[-1].rstrip()])         # Strip newline from last line
 
 class TokenTransformBase:
     """Base class for transformations which examine tokens.
diff --git a/IPython/core/tests/test_inputtransformer2.py b/IPython/core/tests/test_inputtransformer2.py
index 1ff0fd8..61f183c 100644
--- a/IPython/core/tests/test_inputtransformer2.py
+++ b/IPython/core/tests/test_inputtransformer2.py
@@ -31,6 +31,16 @@ for a in range(5):
     get_ipython().run_line_magic('ls', '')
 """.splitlines(keepends=True))
 
+CRLF_MAGIC = ([
+    "a = f()\n",
+    "%ls\r\n",
+    "g()\n"
+], (2, 0), [
+    "a = f()\n",
+    "get_ipython().run_line_magic('ls', '')\n",
+    "g()\n"
+])
+
 MULTILINE_MAGIC_ASSIGN = ("""\
 a = f()
 b = %foo \\
@@ -190,6 +200,7 @@ def test_find_magic_escape():
 def test_transform_magic_escape():
     check_transform(ipt2.EscapedCommand, MULTILINE_MAGIC)
     check_transform(ipt2.EscapedCommand, INDENTED_MAGIC)
+    check_transform(ipt2.EscapedCommand, CRLF_MAGIC)
 
 def test_find_autocalls():
     for case in [AUTOCALL_QUOTE, AUTOCALL_QUOTE2, AUTOCALL_PAREN]:
diff --git a/IPython/core/tests/test_inputtransformer2_line.py b/IPython/core/tests/test_inputtransformer2_line.py
index 41b6ed2..263bbd9 100644
--- a/IPython/core/tests/test_inputtransformer2_line.py
+++ b/IPython/core/tests/test_inputtransformer2_line.py
@@ -114,3 +114,13 @@ def test_leading_empty_lines():
         nt.assert_equal(
                 ipt2.leading_empty_lines(sample.splitlines(keepends=True)),
                 expected.splitlines(keepends=True))
+
+CRLF_MAGIC = ([
+    "%%ls\r\n"
+], [
+    "get_ipython().run_cell_magic('ls', '', '')\n"
+])
+
+def test_crlf_magic():
+    for sample, expected in [CRLF_MAGIC]:
+        nt.assert_equal(ipt2.cell_magic(sample), expected)
\ No newline at end of file