The incidents occurred between 2001 and 2003, officials allege.
The 44-year-old actor faces three counts of rape by force or fear. He was arrested at 11:30 a.m. Wednesday and released from custody about 2:45 p.m. after posting $3.3 million bail, according to booking records.
Masterson allegedly raped a 23-year-old woman between January and December 2001, according to a criminal complaint against him. He is also accused of raping a 28-year-old woman in April 2003. Sometime between October and December of that year, he allegedly raped a 23-year-old woman who he invited to his home.