Here is another way with leading '0' for all of them.
$secCount = 10000;
$hours = str_pad(floor($secCount / (60*60)), 2, '0', STR_PAD_LEFT);
$minutes = str_pad(floor(($secCount - $hours*60*60)/60), 2, '0', STR_PAD_LEFT);
$seconds = str_pad(floor($secCount - ($hours*60*60 + $minutes*60)), 2, '0', STR_PAD_LEFT);
It is an adaptation from the answer of Flaxious.