The Caltrain Express (CTX) project was implemented from 2002 to 2004 and led to the establishment of commuter railroad Caltrain's "Baby Bullet" express service, which shortened the transit time between San Francisco and San Jose, and certain stations in between. New locomotives and rolling stock were purchased for dedicated express service, bypassing most stations; quad-track overtake sections were added in two locations along the Peninsula Corridor right-of-way to allow express trains to pass slower local trains that were making all stops; tracks were also upgraded with continuous-welded rail; a centralized traffic control system was added; and crossovers were added every few miles to allow single-tracking trains around disabled trains. Congresswoman Jackie Speier, then serving as a California State Senator, is credited with securing the funding for CTX and one of the new locomotives acquired for the project is named for her as a result.
In 1997, after plans to extend Caltrain to downtown San Francisco were put on hold, the Peninsula Corridor Joint Powers Board (PCJPB) started the Rapid Rail Study, which was published as a draft in October 1998. The 1998 Rapid Rail Study prioritized planned capital improvements to implement the 1997 Caltrain 20-Year Strategic Plan, which sought to improve service and increase ridership, which was assumed to correspond directly to improved service (through decreased transit times and increased train frequencies). The highest-priority projects were intended to rehabilitate the line to "reverse decades of deferred maintenance" and enhance the line by adding overtake tracks to implement express service. After rehabilitation and enhancement, the Rapid Rail Study called for electrification of the line.
Proposed rehabilitation work included rebuilding tracks and grade crossings to enable Caltrain to raise the systemwide speed limit to 79 to 90 mph (127 to 145 km/h) and replacing bridges, culverts, and signals. The initial enhancement projects included adding third overtake tracks in Burlingame (between the stations at Millbrae and San Mateo, for northbound trains) and San Mateo (between 9th Avenue and Hillsdale, for southbound trains) to allow express trains to pass slower all-stop local trains, and adding a third turnback track in Palo Alto to allow more frequent short-line service. In 1999, PCJPB published an implementation plan for the Rapid Rail Study which called for a $280 million investment from the three counties served by Caltrain.