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| 2001 || September || Station facilities || BART closes restrooms at all stations following a recommendation from the Department of Homeland Security in the wake of the {{w|September 11 attacks}}. Soon, all but the underground restrooms (ten stations total) would be reopened. Discussions on reopening the underground stations, with a more "secure" remodeled layout would continue till 2017.<ref>{{cite web|url = http://sanfrancisco.cbslocal.com/2015/06/25/could-bart-finally-reopen-its-bathrooms-at-underground-stations/|title = Could BART Finally Reopen Its Bathrooms At Underground Stations?|date = June 25, 2015|accessdate = October 23, 2017|publisher = CBS Local}}</ref><ref>{{cite web|url = http://www.mercurynews.com/2017/03/31/roadshow-bart-may-reopen-bathrooms-at-two-stations/|title = Roadshow: BART bathrooms to reopen with new ‘secure’ layout|date = March 31, 2017|accessdate = October 23, 2017|publisher = Mercury News}}</ref><ref>{{cite web|url = http://bartrage.com/node/1349|title = Where are your restrooms?|publisher = BART Rage}}</ref>
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| 2001 || || Connectivity (ceullarcellular) || The BART Board authorizes staff to develop a privately financed underground wireless telecommunications system to provide cell phone use and Internet access for the entire BART system.<ref name=bart-transbay-cellular/> In response to people concerned about others using cellphones and distracting others during the commute, BART condicts a pair of polls. The September 11 attacks, where cellphones are highlighted as having been useful in dealing with the situation, are believed to be a factor that makes people more in favor of improving cellular connectivity on BART.<ref name=sfgate-underground-not-unconnected/>
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| 2002 || || Fare collection || Translink, the smart card payment system, launches.<ref name=clipper-launch-brochure/> ||
| 2005 || October 15 || Highway transportation shutdown || Caltrans shuts down all eastbound lanes on the [[w:San Francisco–Oakland Bay Bridge|San Francisco–Oakland Bay Bridge]] over the weekend for earthquake retrofit work, increasing the pressure on BART to carry transbay traffic. BRT runs transbay trains around the clock to serve transbay travelers.<ref>{{cite web|url = https://www.bart.gov/news/articles/2005/news20051011|title = BART runs around the clock during the October 15th weekend|date = October 11, 2005|accessdate = April 27, 2019|publisher = Bay Area Rapid Transit}}</ref><ref name=bart-40-years/> || Transbay Tube
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| 2005 || || Connectivity (cellular) || BART expands cell service to the non-downtown San Francisco underground stations, and later to the entire underground line in San Francisco.<ref name=bart-transbay-cellular/><ref name=sfgate-underground-not-unconnected>{{cite web|url = https://www.sfgate.com/bayarea/article/Underground-but-not-unconnected-BART-offers-2594271.php|title = Underground, but not unconnected -- BART offers wireless service to riders|last = Cabanatuan|first = Michael|date = November 19, 2005|accessdate = April 27, 2019|publisher = San Francisco Chronicle}}</ref> || 16th Street/Mission, 24th Street/Mission, Glen Park, Balboa Park
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| 2006 || March 27, 28, and 29 || Service disruption || BART has to shut down service for several hours on each of Monday March 27, Tuesday March 28, and Wednesday March 29, due to computer shutdowns. The firs two incidents are due to a problem with the latest version of software that was installed. The third instance is an unexpected side-effect of the work to configure a backup system for faster recovery in such incidents. In an article on April 5 on its website, BART offers a postmortem and plans for improving in the future.<ref>{{cite web|url = https://www.bart.gov/news/articles/2006/news20060405|title = About recent service interruptions, what we're doing to prevent similar problems in the future|date = April 5, 2006|accessdate = April 27, 2019|publisher = Bay Area Rapid Transit}}</ref>
| 2008 || January 1 || Fares || New, increased BART fares are effective from this date. The minimum fare is now $1.50 (up from $1.25) and the excursion fare is now $4.90 (up from $4.40).<ref>{{cite web|url = https://www.bart.gov/sites/default/files/docs/BART010108.pdf|title = BART Fares and Schedules: Effective January 1, 2008|accessdate = July 5, 2017}}</ref> ||
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| 2008 || July 21 || Connectivity (cellular) || BART works with cellphone carrier MetroPCS to add MetroPCS to the list of carriers (previous list: Sprint, Verizon, AT&T and T-Mobile) with service in the underground San Francisco portion of its line .<ref>{{cite web|url = https://www.bart.gov/news/articles/2008/news20080721b|title = Underground cellphone coverage on BART expands|date = July 21, 2008|accessdate = April 27, 2019|publisher = Bay Area Rapid Transit}}</ref> || All of the underground San Francisco system (stations: Embarcadero, Montgomery, Powell Street, Civic Center, 16th Street/Mission, 24th Street/Mission, Glen Park, Balboa Park)
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| 2008 || July, August || Information for riders || BART gets a Twitter account (@SFBART) in July. The earliest surviving tweet is from August 13.<ref>{{cite web|url = https://twitter.com/SFBART/status/886393658|title = Heard on BART: One rider giving another a book recommendation - "The Inheritance of Loss" by Kiran Desai. What are you reading on BART?|publisher = Bay Area Rapid Transit|date = JAugust 13, 2008|accessdate = April 27, 2019}}</ref> Over the years, BART would use its Twitter account to complement its other means of providing news and real-time updates to riders, reaching over 30,000 tweets by early 2019.
