The cats survived almost a week without food and water. One cat's eye is almost swollen shut but is expected to be OK.
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The Napa Police Department says the van was stolen on February 26 and found March 2 in Napa. No arrests have been made.
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Meanwhile, ABC7 obtained surveillance video that shows the moment someone took off with the van while the feral cats were inside.
Margo Cassidy, President of Whiskers, Tails and Ferals in Napa, said someone biked up to their van and broke into it, taking off with it.
"We are just so excited and just so elated that we have the cats back," Cassidy said. "They're living lives. They're living beings. Who could care less about the van? It was all about the cats."
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The organization rescues cats and dogs from high-kill shelters and rehabs feral kitties.
"(The cats) were trapped and ready to go to the clinic the following day," Cassidy said. "That's typically how T & R groups do it. You trap them. You leave them in your car and you take them early in the morning because sometimes you don't get done until midnight, sometimes 2 o'clock in the morning."
MORE: Bay Area shelters make plea to pet owners as facilities overflow with abandoned animals
The team at Whiskers, Tails and Ferals is thanking everyone who helped find the stolen cats.
Someone even pitched in with a $5,000 reward to help find them.
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There's a chance one cat may be adopted out, Cassidy said. That's because that cat is friendly.
But they are feral cats and the plan is for them to be taken to the clinic, spayed and neutered, rehabbed and sent back to where they came from.