diff --git a/docs/use/myst-notebooks.md b/docs/use/myst-notebooks.md
index 1292771..ec60971 100644
--- a/docs/use/myst-notebooks.md
+++ b/docs/use/myst-notebooks.md
@@ -53,6 +53,22 @@ If **both** an `.ipynb` and a `.md` file exist in your book's folders, then
 the `.md` file will take precedence!
 ```
 
+### The Jupyter Book MyST CLI
+
+Jupyter Book has a small CLI to provide common functionality for manipulating and
+creating MyST markdown files that synchronize with Jupytext. To add Jupytext syntax
+to a markdown file (that will tell Jupytext it is a MyST markdown file), run the
+following command:
+
+```bash
+jupyter-book myst init mymarkdownfile.md --kernel kernelname
+```
+
+If you do not specify `--kernel`, then the default kernel will be used *if there is
+only one available*. If there are multiple kernels available, you must specify one
+manually.
+
+
 ## Structure of MyST notebooks
 
 Let's take a look at the structure that Jupytext creates, which you may also use
diff --git a/jupyter_book/commands/__init__.py b/jupyter_book/commands/__init__.py
index 7fa9179..55e291a 100644
--- a/jupyter_book/commands/__init__.py
+++ b/jupyter_book/commands/__init__.py
@@ -10,7 +10,7 @@
 from ..sphinx import build_sphinx
 from ..toc import build_toc
 from ..pdf import html_to_pdf
-from ..utils import _message_box, _error
+from ..utils import _message_box, _error, init_myst_file
 
 
 @click.group()
@@ -91,7 +91,7 @@ def build(path_book, path_output, config, toc, warningiserror, build):
     if exc:
         _error(
             "There was an error in building your book. "
-            "Look above for the error message.",
+            "Look above for the error message."
         )
     else:
         # Builder-specific options
@@ -221,3 +221,21 @@ def toc(path, filename_split_char, skip_text, output_folder):
     output_file.write_text(out_yaml)
 
     _message_box(f"Table of Contents written to {output_file}")
+
+
+@main.group()
+def myst():
+    """Manipulate MyST markdown files."""
+    pass
+
+
+@myst.command()
+@click.argument("path", nargs=-1, type=click.Path(exists=True, dir_okay=False))
+@click.option(
+    "--kernel", help="The name of the Jupyter kernel to attach to this markdown file."
+)
+def init(path, kernel):
+    """Add Jupytext metadata for your markdown file(s), with optional Kernel name.
+    """
+    for ipath in path:
+        init_myst_file(ipath, kernel, verbose=True)
diff --git a/jupyter_book/tests/test_utils.py b/jupyter_book/tests/test_utils.py
new file mode 100644
index 0000000..b463878
--- /dev/null
+++ b/jupyter_book/tests/test_utils.py
@@ -0,0 +1,28 @@
+from pathlib import Path
+from jupyter_book.utils import init_myst_file
+import pytest
+
+
+def test_myst_init(tmpdir):
+    """Test adding myst metadata to text files."""
+    path = Path(tmpdir).joinpath("tmp.md").absolute()
+    text = "TEST"
+    with open(path, "w") as ff:
+        ff.write(text)
+    init_myst_file(path, kernel="python3")
+
+    # Make sure it runs properly. Default kernel should be python3
+    new_text = path.read_text()
+    assert "format_name: myst" in new_text
+    assert "TEST" == new_text.strip().split("\n")[-1]
+    assert "name: python3" in new_text
+
+    # Non-existent kernel
+    with pytest.raises(Exception) as err:
+        init_myst_file(path, kernel="blah")
+    assert "Did not find kernel: blah" in str(err)
+
+    # Missing file
+    with pytest.raises(Exception) as err:
+        init_myst_file(path.joinpath("MISSING"), kernel="python3")
+    assert "Markdown file not found:" in str(err)
diff --git a/jupyter_book/utils.py b/jupyter_book/utils.py
index b00cfa7..923a601 100644
--- a/jupyter_book/utils.py
+++ b/jupyter_book/utils.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 from textwrap import dedent
+from jupyter_client.kernelspec import find_kernel_specs
 
 SUPPORTED_FILE_SUFFIXES = [".ipynb", ".md", ".markdown", ".myst", ".Rmd", ".py"]
 
@@ -62,3 +63,52 @@ def _error(msg, kind=None):
         kind = ValueError
     box = _message_box(msg, color="red", doprint=False)
     raise kind(box)
+
+
+##############################################################################
+# MyST + Jupytext
+
+
+def init_myst_file(path, kernel, verbose=True):
+    """Initialize a file with a Jupytext header that marks it as MyST markdown.
+
+    Parameters
+    ----------
+    path : string
+        A path to a markdown file to be initialized for Jupytext
+    kernel : string
+        A kernel name to add to the markdown file. See a list of kernel names with
+        `jupyter kernelspec list`.
+    """
+    try:
+        from jupytext.cli import jupytext
+    except ImportError:
+        raise ImportError(
+            "In order to use myst markdown features, " "please install jupytext first."
+        )
+    if not Path(path).exists():
+        raise FileNotFoundError(f"Markdown file not found: {path}")
+
+    kernels = list(find_kernel_specs().keys())
+    kernels_text = "\n".join(kernels)
+    if kernel is None:
+        if len(kernels) > 1:
+            _error(
+                "There are multiple kernel options, so you must give one manually."
+                " with `--kernel`\nPlease specify one of the following kernels.\n\n"
+                f"{kernels_text}"
+            )
+        else:
+            kernel = kernels[0]
+
+    if kernel not in kernels:
+        raise ValueError(
+            f"Did not find kernel: {kernel}\nPlease specify one of the "
+            f"installed kernels:\n\n{kernels_text}"
+        )
+
+    args = (str(path), "-q", "--set-kernel", kernel, "--set-formats", "myst")
+    jupytext(args)
+
+    if verbose:
+        print(f"Initialized file: {path}\nWith kernel: {kernel}")
diff --git a/setup.py b/setup.py
index 2acf5ba..338272b 100644
--- a/setup.py
+++ b/setup.py
@@ -19,6 +19,7 @@
     "beautifulsoup4",
     "matplotlib",
     "pytest-regressions",
+    "jupytext",
 ] + doc_reqs
 setup(
     name="jupyter-book",