According to investigators, Samuel James Gulick, 18, of Middletown, drove to the facility in Newark on January 3 and spray painted the phrase "Deus Vult" in red letters before lighting an object on fire and throwing it through the front window.
The object exploded and Gulick ran away, authorities said. The fire burned for about a minute before self-extinguishing.
The explosion damaged the front window and porch of the building.
Gulick was arrested by the FBI without incident on Saturday.
He is now charged with maliciously damaging a building used in interstate commerce through the use of fire or destructive device, intentionally damaging a facility that provides reproductive health services and possession of an unregistered destructive device under the National Firearms Act.
If convicted of the most serious offense, he faces a statutory minimum of five years and a maximum of 20 years in prison and a $250,000 fine.