Did this several months ago after experiencing several dead battery situations. Here is the best pictorial guide available, and what I primarily used to get through the ordeal. More below.
As most who own them know, the Prius actually contains 2 batteries. The big “traction” battery sits under and behind the back seat and is used to power the car’s electric motor. These usually last over 200,000 miles or 7 years (or both). They cost a small fortune to replace (a new, uninstalled, traction battery goes for around $2,000 exclusive of shipping — which is quite expensive).
The smaller auxiliary battery is tucked away on one side of the “trunk” (the hatch compartment), underneath a protective plastic shield and surrounded by power cables, ventilation tubes and retaining brackets. This directly powers the car’s computer and electrical systems, including the relay that switches the system to the traction battery when the car is set to “ready” by depressing the start button. The auxiliary battery is there for safety reasons. In the event the car is disabled anyone working near it (like first responders to an accident) don’t have to worry about being fried by contact with the higher voltage traction battery. The auxiliary battery shipped with the car usually lasts around 4 – 5 years. The fact that I got to 6 with mine is actually pretty remarkable.
I ordered my replacement auxiliary battery from eLearnAid, on this page. This is an Optima D51 “yellow top”. It’s known as a “deep charging” battery, designed to be much longer lasting than an ordinary auto battery and costs around $175.
The installation took the better part of a Saturday morning, mostly because of my natural clumsiness and caution. In the end everything worked out fine, and after several months I’m still getting a solid 14v after riding around for awhile.