At the time, Indonesia lost its investor confidence due to concerns regarding to unstable domestic situations in the early 2000s, so the MRT construction was unable to be realized yet.

Among those four, the bus rapid transit was considered the most likely to be realized in a short time because it didn't require foreign investments.

[9] The Institute for Transportation and Development Policy (ITDP) was an important party accompanying the BRT planning process.

Apart from the private sector, there were several other parties that also supporting this project, including the United States Agency for International Development (USAID) and University of Indonesia's Center for Transportation Studies (UI–CTS).

The buses were given lanes restricted to other traffic and separated by concrete blocks on the streets that became part of the busway routes.

[19] Transjakarta has undertaken an ambitious plan to expand its electric bus (e-bus) fleet to 10,000 units over the decade and to have all of its buses electric-powered by 2030.

The characteristics of Transjakarta listed in an Asian Development Bank study are:[20] 15 corridors were initially planned, 14 of which are currently operational.

Transjakarta buses have electronic boards and speakers that announce the name of shelters in Indonesian and English, bi-directional radio transceivers for communication between drivers and control centers, at least four mandatory CCTV cameras per bus, and automatic air freshener dispensers to keep the air fresh during rush hours.

Payment is made through electronic tapping equipment on board the buses, and the service is not integrated into the main BRT system.

The Mercedes-Benz OH and Hino RG air-conditioned buses operated in Corridor 1 are painted red and yellow, with a picture of a young brahminy kite, which looks similar to a bald eagle grasping a tree branch with three salaks on it.

Due to various coach builders being involved and design tweaks applied over time, the exterior and interior appearance, quality, and comfort varies between buses operating in the same corridor.

Older shelters usually lack sanitary facilities, although newer ones include large and disable-friendly restrooms and praying rooms.

According to a report from the Indonesian Consumers Protection Foundation in 2011, the most common complaint from passengers about the service offered by Transjakarta was the long wait times for buses at some of the main shelters.

[41] Tosari and Bundaran HI ASTRA shelters are revitalized into an iconic "twin cruise ships that anchored at the Selamat Datang Monument", with the upper floor being a commercial area and photobooth balcony.

The revitalisation includes full reconstruction of the shelters with the new style, such as half-height cream-colored concrete-constructed walls, concrete-made floors, and the inclusion of sanitary facilities.

[43] These temporary stations are small and some of them are made of two separate buildings for opposing directions that require passengers to tap and pay again to cross between, making them unsuitable to be a transit point and as such they only serve Corridor 1.

Passengers who wish to change direction or transit to other corridors do not need to pay again, provided they do not exit the paid area and complete the whole journey in one trip.

[47] In April and May 2014, the Transjakarta management started compulsory use of e-tickets at several terminus in the system, based on news that the BCA Flazz Card could also be used in Jabodetabek Commuter Train.

[51] The TJ Card, introduced in January 2018, provides free fares for their holders and is available for seniors above 60, residents of the Thousand Islands Regency, disabled persons, low-income households, teachers, mosquito controllers and mosque caretakers in addition to members of the Indonesian National Armed Forces and the Police.

[52] In the early days of feeder (Non-BRT) routes, passengers could pay cash to the bus conductor or use a prepaid card issued by a specific bank.

On 2 October 2020, Transjakarta launched Tije, an app that allowed passengers to buy tickets using QR codes.

However, the agreement was short lived, as Transjakarta terminated its contract in January 2024, leaving Tije app as the sole platform for its bus tracking.

This situation is at odds with one of the objectives of Transjakarta, which was to reduce traffic jam during rush hours by persuading private car owners to use comfortable public transport.

In May 2013, it was reported that the system was losing passengers due to unpredictable service frequency, worsening travel times, and poor maintenance of the infrastructure and vehicles.

In 2011, in an effort to stop non-Transjakarta vehicles using the bus lanes, the Jakarta Police Chief suggested that Transjakarta buses should run against the direction of traffic flow.

[66] On 12 January 2012, a policeman from the Indonesian Police Headquarters, who was hired by Securicor, fired his gun near the ear of a Transjakarta officer after threatening to kill him.

[70] In 2014, a corruption investigation began over series of accidents related to poor conditions of new vehicles through fraudulent procurement of more than one trillion IDR.

[71] Pristono argued that he was only working under the supervision of then governor Joko Widodo on the procurement project,[72] and accusing him liable for the legal prosecution as he had the responsibility over financial budget abuses involved in his administration.

[78] Demonstrations opposing a bill draft in October 2020 turned violent and multiple BRT shelters became targets.

In 2016, Kopaja AC buses (under pilot integration program with Transjakarta) collided with Corridor 1 bus at Monas station triggering a chain collision and 2 fatal injuries.