There is probably some way to do this via MySQL, however, the easy (and reliable) way is using PHP's microtime function, which returns the current time as milliseconds.
microtime() returns the current Unix timestamp with microseconds. This function is only > available on operating systems that support the gettimeofday() system call.
getasfloat - When called without the optional argument, this function returns the string "msec sec" where sec is the current time measured in the number of seconds since the Unix Epoch (0:00:00 January 1, 1970 GMT), and msec is the microseconds part. Both portions of the string are returned in units of seconds.
If the optional get_as_float is set to TRUE then a float (in seconds) is returned.
Some example code:
$sql = '...';
$msc = microtime(true);
mysql_query($sql);
$msc = microtime(true)-$msc;
echo $msc . ' s'; // in seconds
echo ($msc * 1000) . ' ms'; // in millseconds
