KCRC estimated the construction cost of Ma On Shan Rail would be HK$10 billion. The line starts at Tai Wai station in Tai Wai, Shatin and ends at Wu Kai Sha Station, Wu Kai Sha, totalling 11.4 km or 16 minutes of journey time. It has nine stations, with a maintenance depot at Tai Wai. Construction began on 12 February 2001 and the line opened on 21 December 2004, 3 days earlier than the proposed opening date. When it was operating as part of the KCR system, the interchange with the East Rail Line at Tai Wai did not have ticket gates between the Ma On Shan line and East Rail Line platforms. A trip from either line to the other counted as one ride. It is estimated the line handled 190,000 passengers in the first year of service.
Most of the line, including stations, was built on a viaduct on reserved land (right-of-way) along the eastern side of Sha Tin and Ma On Shan (administratively within Sha Tin District.) Although currently the trains are only in four-car configuration, most platforms have provision for eight-car trains for when patronage increases.
The fare for a trip on the line varies from HK$3.2 to HK$5.8 depending on the distance travelled. The fare from Ma On Shan to East Rail Line stations in Kowloon varies from HK$6.2 to HK$8.4.
Over a thousand passengers went to Tai Wai to take the first train on the first day of service. However, just an hour after service commenced, one train suffered minor door defects, causing a three-minute delay. After the opening of the Ma On Shan Line, the usage of buses and taxis in the area decreased by as much as 50%. It was reported that some bus routes operated by KMB saw a decrease of ridership by one-third just a few days after the railway opened.
Road and rail traffic in Hong Kong move on the left, but Ma On Shan Line is an exception. This line is aligned to the east of East Rail Line, and the two southbound tracks are immediately next to each other at their connection in Tai Wai. This design is to speed up interchange to the East Rail Line to Kowloon during the morning commute. Therefore, the Ma On Shan Line moves on the right.
Although Ma On Shan Rail is defined as a medium capacity system, KCRC has arranged 18 sets of Kinki Sharyo EMU SP1950 trains, built by Kinki Sharyo, running on the system in a four-car configuration. The train is the same model (with different contract code, SP1900) as those serving on the high capacity East Rail Line and West Rail Line, which run a 12-car and a seven-car configuration respectively. This model has the maximum running speed of 130 km/h, but trains will only reach a maximum service speed of 100 km/h; travelling between Shek Mun Station and Tai Shui Hang Station, when it is on ground level between Tate's Cairn Highway. In fact, most of the time the trains on the line only travel between 55–75 km/h. The Tai Wai Depot maintains the trains servicing this line.