You should simply be able to answer ‘yes‘, which will update your ~/.ssh/known_hosts file.

---

A better approach, to avoid any MITM (Man-In-The-Middle) attack, would be (as commented below by Mamsds) to verify GitHub’s public key first (see “GitHub’s SSH key fingerprints“) and, if you find a match, then you can answer ‘yes’.

Example:

ssh-keyscan -t ecdsa github.com 2>&1 |ssh-keygen -lf -
256 SHA256:uNiVztksCsDhcc0u9e8BujQXVUpKZIDTMczCvj3tD2s github.com (ECDSA)

---

After that, you can use a GitHub SSH URL (provided you have generated the SSH public/private keys, and registered the public one to your GitHub profile)

Note: the ssh key generation should use the base64 old PEM format (option -m PEM), rather than the new current 70 chars OpenSSH one.
See “What is the correct format for private key in Credentials“:

ssh-keygen -m PEM -t rsa -P "" -f afile

That or you can switch to an HTTPS URL.

---

Update March 2023:

GitHub updated their RSA SSH host key

At approximately 05:00 UTC on March 24, out of an abundance of caution, we replaced our RSA SSH host key used to secure Git operations for GitHub.com.

We did this to protect our users from any chance of an adversary impersonating GitHub or eavesdropping on their Git operations over SSH. This key does not grant access to GitHub’s infrastructure or customer data. This change only impacts Git operations over SSH using RSA.
Web traffic to GitHub.com and HTTPS Git operations are not affected.

Only GitHub.com’s RSA SSH key was replaced. No change is required for ECDSA or Ed25519 users

If you see the following message when connecting to GitHub.com via SSH, then read onward.

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
SHA256:uNiVztksCsDhcc0u9e8BujQXVUpKZIDTMczCvj3tD2s.
Please contact your system administrator.
Add correct host key in ~/.ssh/known_hosts to get rid of this message.
Host key for github.com has changed and you have requested strict > checking.
Host key verification failed.

If you see the above message, you’ll need to remove the old key by running this command:

$ ssh-keygen -R github.com

Or manually updating your ~/.ssh/known_hosts file to remove the old entry.

Then, you can manually add the following line to add the new RSA SSH public key entry to your ~/.ssh/known_hosts file:

github.com ssh-rsa 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

Or automatically update GitHub.com’s RSA SSH key in your ~/.ssh/known_hosts, by running the following in your terminal:

$ ssh-keygen -R github.com
$ curl -L https://api.github.com/meta | jq -r '.ssh_keys | .[]' | sed -e 's/^/github.com /' >> ~/.ssh/known_hosts

You can verify that your hosts are connecting via our new RSA SSH key by confirming that you see the following fingerprint:

SHA256:uNiVztksCsDhcc0u9e8BujQXVUpKZIDTMczCvj3tD2s

GitHub Actions users may see failed workflow runs if they are using actions/checkout with the ssh-key option.
We are updating the actions/checkout action in all our supported tags, including @v2, @v3, and @main.
If you pin the action to a commit SHA and use the ssh-key option, you’ll need to update your workflow. You can read more about this process in our official documentation for Actions security hardening.

For more information, please visit our official documentation on GitHub’s SSH public key fingerprints.

So:

What happened and what actions have we taken?

This week, we discovered that GitHub.com’s RSA SSH private key was briefly exposed in a public GitHub repository.

We immediately acted to contain the exposure and began investigating to understand the root cause and impact.
We have now completed the key replacement, and users will see the change propagate over the next thirty minutes.
Some users may have noticed that the new key was briefly present beginning around 02:30 UTC during preparations for this change.

Please note that this issue was not the result of a compromise of any GitHub systems or customer information.
Instead, the exposure was the result of what we believe to be an inadvertent publishing of private information. We have no reason to believe that the exposed key was abused, and took this action out of an abundance of caution.

---

As noted by bk2204‘sanswer:

Some versions of OpenSSH include the host key for the IP address as well as for the hostname.
This is rather unhelpful, as IP addresses can change with DNS, but hostname tend to be more stable.

To remove the old key entirely:

# linux
sed -i -e '/AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31\/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi\/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==/d' ~/.ssh/known_hosts

# MacOS
sed -i '' -e '/AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31\/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi\/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==/d' ~/.ssh/known_hosts

# Windows
sed -i -e "/AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31\/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi\/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==/d" %USERPROFILE%\.ssh\known_hosts

The last command (for Windows) can be done with the %PATH% modified with:

set "GH=%ProgramFiles%\Git"
set "PATH=%GH%\bin;%GH%\cmd;%GH%\usr\bin;%GH%\mingw64\bin;%GH%\mingw64\libexec\git-core;%PATH%"

---

To remove any GitHub IP address from your known_hosts file, see discussion 50878:

For anyone running into repeated ECDSA host key for 'github.com' differs from the key for the IP address / Offending key for IP issues and you can’t grep IPs in known_hosts because you have hashed entries, I have created a Gist listing all Github git IPv4 addresses (as of Fri Mar 24 16:33:22 UTC 2023), generated from CIDRs listed in https://api.github.com/meta:

https://gist.github.com/a-abella/fb31a028943b804e8ada6cda4efbe9b6

You can loop over these and feed them to ssh-keygen -R.
A script with optional known_hosts file path argument is available here: https://gist.github.com/a-abella/9d6c91a56a892e4c74933d17d380aa01. The only dependency is curl.

If you want a one-liner (though the standard you-shouldn’t-pipe-scripts-from-the-internet warnings apply):

curl -s https://gist.githubusercontent.com/a-abella/9d6c91a56a892e4c74933d17d380aa01/raw/0bcaef131f94e4938cb659d744c3019fd814643e/strip_github.sh | bash -s -- $HOME/.ssh/known_hosts