diff --git a/jupytext/cli.py b/jupytext/cli.py
index b3a5626b7..72df6964c 100644
--- a/jupytext/cli.py
+++ b/jupytext/cli.py
@@ -324,7 +324,11 @@ def writef_git_add(notebook_, nb_file_, fmt_):
             # Read paired notebooks
             if args.sync:
                 set_prefix_and_suffix(fmt, notebook, nb_file)
-                notebook, inputs_nb_file, outputs_nb_file = load_paired_notebook(notebook, fmt, nb_file, log)
+                try:
+                    notebook, inputs_nb_file, outputs_nb_file = load_paired_notebook(notebook, fmt, nb_file, log)
+                except NotAPairedNotebook as err:
+                    sys.stderr.write('[jupytext] Warning: ' + str(err) + '\n')
+                    continue
 
             # II. ### Apply commands onto the notebook ###
             # Pipe the notebook into the desired commands
@@ -473,12 +477,17 @@ def set_prefix_and_suffix(fmt, notebook, nb_file):
                 continue
 
 
+class NotAPairedNotebook(ValueError):
+    """An error raised when a notebook is not a paired notebook"""
+    pass
+
+
 def load_paired_notebook(notebook, fmt, nb_file, log):
     """Update the notebook with the inputs and outputs of the most recent paired files"""
     formats = notebook.metadata.get('jupytext', {}).get('formats')
 
     if not formats:
-        raise ValueError("'{}' is not a paired notebook".format(nb_file))
+        raise NotAPairedNotebook("'{}' is not a paired notebook".format(nb_file))
 
     max_mtime_inputs = None
     max_mtime_outputs = None
diff --git a/tests/test_cli.py b/tests/test_cli.py
index ce475b7b5..b38d5dbd5 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -590,16 +590,17 @@ def test_paired_paths(nb_file, tmpdir, capsys):
 
 
 @pytest.mark.parametrize('nb_file', list_notebooks('ipynb_py'))
-def test_sync(nb_file, tmpdir):
+def test_sync(nb_file, tmpdir, capsys):
     tmp_ipynb = str(tmpdir.join('notebook.ipynb'))
     tmp_py = str(tmpdir.join('notebook.py'))
     tmp_rmd = str(tmpdir.join('notebook.Rmd'))
     nb = read(nb_file)
     write(nb, tmp_ipynb)
 
-    # Test that sync fails when notebook is not paired
-    with pytest.raises(ValueError, match='is not a paired notebook'):
-        jupytext(['--sync', tmp_ipynb])
+    # Test that sync issues a warning when the notebook is not paired
+    jupytext(['--sync', tmp_ipynb])
+    _, err = capsys.readouterr()
+    assert 'is not a paired notebook' in err
 
     # Now with a pairing information
     nb.metadata.setdefault('jupytext', {})['formats'] = 'py,Rmd,ipynb'
@@ -641,15 +642,16 @@ def test_sync(nb_file, tmpdir):
 
 @requires_pandoc
 @pytest.mark.parametrize('nb_file', list_notebooks('ipynb_py', skip='(Notebook with|flavors)'))
-def test_sync_pandoc(nb_file, tmpdir):
+def test_sync_pandoc(nb_file, tmpdir, capsys):
     tmp_ipynb = str(tmpdir.join('notebook.ipynb'))
     tmp_md = str(tmpdir.join('notebook.md'))
     nb = read(nb_file)
     write(nb, tmp_ipynb)
 
-    # Test that sync fails when notebook is not paired
-    with pytest.raises(ValueError, match='is not a paired notebook'):
-        jupytext(['--sync', tmp_ipynb])
+    # Test that sync issues a warning when the notebook is not paired
+    jupytext(['--sync', tmp_ipynb])
+    _, err = capsys.readouterr()
+    assert 'is not a paired notebook' in err
 
     # Now with a pairing information
     nb.metadata.setdefault('jupytext', {})['formats'] = 'ipynb,md:pandoc'