The 15 animals travelled in the main cabin of Virgin America flights that left from San Francisco International Airport on Wednesday morning.
Officials from the American Society for the Prevention of Cruelty to Animals met the animals at New York's John F. Kennedy International Airport to help find them homes.
San Francisco animal control officials say Chihuahuas are in abundance at California animal shelters, but they're in demand in other states like New York.
The dogs will be made available for adoption next week after full medical assessments.
Experts say pop culture is to blame for the overpopulation of the dogs in California, with fans imitating Chihuahua-toting celebrities like Paris Hilton.