HOW TO: In PHP the MySQL Client API version doesn’t match the MySQL Server version

This is a fairly common situation. The short answer is that you usually don’t need to fix anything. This is a non-issue.  As long as your MySQL and MySQL Client have the same major version, you can and probably should just ignore the issue. There are no compatibility or performance issues involved.

This situation occurs when you use a package installer such as Yum to install a previously compiled version of PHP rather than compiling the version locally yourself. The package creator will have compiled PHP with a version the MySQL client that is compatible with that major release of MySQL.

To quote a 2008 article from the IUS Community project:

That said, I can tell you that in the last 4+ years of providing packages in this ‘mixed’ kind of fashion… we’ve never really come across any major issues of using php built against an older version of mysql… talking to a new version of mysql.

Now if you had to fix this, you could check to see if there is a specially compiled version of PHP with your particular MySQL client installed, but that’s unlikely.  You’re more than likely going to need to recompile php from your command line.  That slightly mismatched version is just the price you pay for convenience.