There were limited pedestrian walkways between the two stations resulting in commuters having to be exposed to the sun and rain and even having to cross the busy Jalan Tun Perak to change from one line to the other.

Opened on 16 December 1996 as part of the first phase of the then STAR system (Phase 1), the Ampang and Sri Petaling Line station was constructed directly above a bridge along Jalan Tun Perak that crosses the Klang River shortly before the Klang River-Gombak River confluence: Its elevated tracks and side platforms are suspended above Jalan Tun Perak, while the ticketing concourses are located over the Klang River, at street level.

The second Masjid Jamek rapid transit station was opened on 1 June 1999 as part of the second phase of the Kelana Jaya Line (then known as PUTRA LRT) (known as Section 2).

In fact, even passengers on the Ampang Line and Sri Petaling who wanted to change their direction of travel at this station could not do so without exiting the turnstiles at the concourse of one side of Jalan Tun Perak, crossing Jalan Tun Perak, and then buying a new ticket at the concourse on the other side of the road to resume their journey.

Called Phase 1 of the Integrated Masjid Jamek station project, the works were completed in October 2008 and the plaza was opened to the public on 15 November 2008.

The underpass, which previously allowed passengers to access Jalan Benteng without needing to cross Jalan Tun Perak from the Kelana Jaya concourse Level B1 was converted into a paid area for passengers transferring between the Kelana Jaya Line and the Ampang Line Station Platform 1 (Sentul Timur-bound).

Trunk bus routes radiate (and converge) here from adjacent suburbs and towns e.g. Sungai Buloh, Ampang, Segambut/Mont Kiara, Kuala Selangor, Kajang, Putrajaya, Subang Jaya and Jalan Klang Lama.

The Lebuh Pudu bus hub located near the Maybank tower and Mydin Sinar Kota branches.