The FBI and the Bureau of Alcohol, Tobacco, Firearms and Explosives joined local authorities in the investigation of the blaze late Monday at the Presidential Women's Clinic.
No one was injured. Details on the extent of damage were not immediately available.
It appeared that lighter fluid or some other accelerant was used to start the blaze, fire department spokesman Phil Kaplan said.
A July 2004 fire damaged another Palm Beach County abortion clinic and a 2003 blaze damaged one in neighboring Broward County.
Florida has had long history of violence against abortion clinics and doctors who perform the operation.
Paul Hill was executed in 2003 for the 1994 murder of a doctor and his escort outside an abortion clinic. Those slayings came one year after Michael Griffin killed a doctor at another Pensacola clinic. He is serving a life sentence.
A decade earlier, two young couples bombed three Pensacola abortion clinics on Christmas Day 1984. No one was injured in those attacks. The two men were released after serving about half of their 10-year federal prison terms. The women received probation.