Bonilla made his debut for Honduras in a May 1991 UNCAF Nations Cup match against Panama and has earned a total of 18 caps, scoring no goals. He has represented his country at the 1991, and 1997 UNCAF Nations Cups, as well as at the 1991, and 1998 CONCACAF Gold Cups. He also was a non-playing squad member at the 1996 CONCACAF Gold Cup.