The first rapid transit station at Sullivan Square opened on June 10, 1901 as part of the Charlestown Elevated rapid transit line, a predecessor to the modern Orange Line. The original elevated station was considered a crown jewel of the "El", along with a similar station complex at Dudley Square in Roxbury. The steel-and-brick structure was designed by Alexander Wadsworth Longfellow Jr. along with the other original elevated stations. It was a polygonal shape about 175 feet (53 m) square, with a glass trainshed spanning an open interior. Sullivan Square and its station are named for James Sullivan, an early 19th-century Governor of Massachusetts and first president of the Middlesex Canal Company.

The station was designed as a major transfer point, with many streetcar lines that had formerly gone downtown truncated to Sullivan. Surface streetcars ran up a ramp to ten stub-end tracks at the level of the elevated stations, allowing cross-platform transfers with elevated trains; lines not terminating at Sullivan used a surface-level loop. 21  Lexington and Boston Street Railway cars from as far away as Lowell ran to Sullivan Square until May 4, 1912, when they were redirected to Harvard station.

Over time, deferred maintenance on the Charlestown Elevated and Sullivan Square station took its toll. A large fire also caused significant damage to the station's upper level on November 1, 1967, and the rail bending shop nearby was destroyed by a fire on January 4, 1975. The Haymarket North Extension was constructed in the early 1970s along the Haverhill Line right-of-way, with a relocated new Sullivan Square station under the elevated I-93 expressway. The Charlestown Elevated closed on April 4, 1975; the Haymarket North Extension opened as far as Sullivan Square on April 7. The new Sullivan station was the terminus of the extension for five months until Wellington opened on September 6, 1975.