At level 80, the trainer gives you a crate, a portable stable. Clicking on it will open the stable and you can choose which pet you want to run with. This has a cooldown of 30 mins.
Most of the time you will not need it. I have had to use it only once, in NAXX, when I had to switch from DPS to DPS/Tank on The Four Horsemen. I switched out my wolf to my bear.