The suspect, identified as Terry King, 39, was arrested outside his home in Longwood late Friday.
The first attack happened close to Webster Avenue in August 2000. A 21-year-old woman was ambushed by a man with a gun who pulled her into a vacant room and raped her, police said.
Ten years later, in November 2010, a man with a gun pulled another 21-year-old woman into a Nissan Pathfinder where he raped her, the NYPD said.
After a DNA analysis in the most recent rape, the NYPD determined that the same man committed both crimes.
Charges against him are pending.