The name points to the Long Island City Courthouse, at 25-10 Court Square.
The courthouse, designed by George Hathorne, was built in the 1870s after the state legislature authorised moving the Queens County seat to Long Island City in 1870; it was rebuilt and enlarged after a fire in 1904. The two stations here were once called 45th Road–Court House Square and Long Island City–Court Square; in 2011 both were renamed simply Court Square.