He arrived with medical supplies and solar energy equipment donated by the Clinton Foundation, which had already transported 76 tonnes of medicine and medical equipment since the storm hit on 20 September.
Mr Clinton also visited health clinics and the island's largest shelter with Puerto Rico Governor Ricardo Rossello.
Mr Rossello said Mr Clinton's visit will help people realise Puerto Rico still needed relief supplies more than two months after he hurricane wreaked havoc on the island.
"It's important to have him here because he has a vision of how to emerge from the emergency phase, establish normalcy and begin to rebuild," Mr Rossello said.
The Clinton Foundation was created in 1997 to support a range of charitable causes, including disaster relief.
The institution has come under fire for accepting donations from banks and foreign entities such as Oman and Kuwait, which have their own agenda for funding relief efforts.
The official death toll from Hurricane Maria is 55, but politicians and experts have said the true number is likely to be significantly higher.
A survey by CNN of funeral homes on the island suggested that as many as 500 had been killed by the storm.
Hurricane Maria caused up to an estimated $95bn (£72bn) in damage. Two months on from the disaster, more than 20 of Puerto Rico's 78 municipalities are still without power and more than 140,000 people have fled for the US mainland.
Associated Press contributed to this report