The football team has been successful since its establishment and has maintained its status as one of India's most successful clubs, having won multiple trophies of national significance such as the Federation Cup, Rovers Cup, Durand Cup, IFA Shield, National Football League and the Domestic League. Mohun Bagan was the first Indian team to defeat a European team, when they defeated the East Yorkshire Regiment, 2-1 to lift the 1911 IFA Shield. Mohun Bagan still carries on an intense local rivalry with Kingfisher East Bengal F.C.
In 1889 near Shyambazar area, there was the famous marble palace, named “Mohun Bagan Villa”. A medium size ground was there in front of this building. At that moment, the players of “Dukhiram Majumder Student's Union” used to play in this ground. But Mr. Majumder then shifted to Laha's field at the Shyampukur area due to some reasons and changed the name of “Dukhiram Majumder Student's Union” to “Aryans”. Some players from Mohun Bagan Villa went to Shyam Square where “Bagbazar Club” was established under the leadership of Young brigade from Sen's House of Bagbazar. But still no club was there for the players who were still continuing to play in the ground of Mohun Bagan Villa. They were not able to compete with the rest of the local clubs. So to provide back up to these players three famous families of Kolkata, the Basu family, Mitra Family and Sen family came forward.
On August 15, 1889 a meeting was organized in the house of the then famous lawyer Mr. Bhupendranath Basu. After the meeting a decision was taken that a club would be formed name “Mohun Bagan Sporting Club” with the existing players playing in Mohun Bagan Villa. The first President and Secretary of Mohun Bagan Sporting Club were Mr. Bhupendranath Basu (1889–1924) and Mr. Jyotindranath Basu (1889–1894).
The name of the club was changed to Mohun Bagan Athletic Club after the recommendations of Mr. F. J. Rowe, the professor of Presidency College. He had remarked that there were no sporting activities, such as shooting or angling.
Mohun Bagan played their first tournament in the year 1893 in Coochbehar Cup. But they did not perform well. The morale of the players was in a very low level but the club officials came forward and backed up the players.
After that time Mohun Bagan participated in lots of tournaments like Coochbehar Cup, Trades Cup but was unable to win any of them. After the opening by the Calcutta Corporation of the public square known as Shyam Square, the club was alloted space there along with Aryans and Baghbazar Club. Thus Shyam Square was the third ground of Mohun Bagan (1895–1900). Some administrative changes took place that time. In 1895, Jyotindranath Mitra became the Honorary Secretary and Jyotindranath Basu became the Vice President. Sir Bhupendra Nath Mitra took over the secretaryship from Jyotindranath Mitra in 1898 and continued until 1900. Mohun Bagan club officials again felt the need to change the ground and that time they decided to move to Kolkata maidan area. But it was very difficult to get a place in maidan area, but due to their candid effort they were able to manage a place for the club. In 1900 Mohun Bagan started to share the ground and tent along with Presidency College (1900–1914). Also in 1900, Subadar Major Sailendranath Basu took the responsibility of secretary post of the club. Since 1900 up to 1914 he ornamented the secretary post. Mr Basu was very strict about the rules and regulations of the club. He was very careful regarding the physical training and fitness of the players and took all the needful steps for the betterment of the football team.
Mohun Bagan won its first trophy, the Coochbehar Cup in the year 1904 and again in 1905. In the same year Mohun Bagan reached the final of Gladstone Cup, held in Chinsurah. The opponent in the final was Dalhousie, the winner of that year IFA Shield defeated Calcutta Football Club by 4-3 in a thrilling final. Mohun Bagan still though managed to win the match 6-1. In 1906, Mohun Bagan got more success. This year the club grabbed the Trades Cup, Gladstone Cup and Coochbehar Cup. These achievements made Mohun Bagan the most prestigious Indian club. In the same year Mohun Bagan participated in Minto Fort Tournament. This tournament was mainly for the British and Army football teams, only Mohun Bagan among the Indian clubs got the invitation to participate in this tournament but there stay was not long. In 1907 Mohun Bagan again won Trades Cup and again in 1908 for a third consecutive time.
Mohun Bagan was the first club in India to win the IFA Shield in 1911 by defeating East Yorkshire Regiment. This match was huge also because Mohun Bagan also became the first Indian club to beat a European club ever. The players of Mohun Bagan played bare-footed against the foreigners, who had proper equipment. It became a turning point in Indian football. 
In 1915 Mohun Bagan played their first match in first division of Calcutta Football League on May 15, 1915 against Calcutta Club. Back then the Calcutta Football League was the number one football league in India. In 1937 Mohun Bagan played its first international match in home country against Englishton Corinthians of England. In 1939 Mohun Bagan became the first ever Indian Calcutta Football League Champion after a long awaiting 25 years.
In 1943 Mohun Bagan created history in the Indian football scenario by implementing an Insurance Scheme for the medical aid of the injured players. Within one year a medical Board was also formed with some doctors. This year Mohun Bagan won the Calcutta Football League for the second time, gaining 39 points in 24 matches. The club also grabbed the Trades Cup this year. The next year Mohun Bagan won the league again.
In 1947 Mohun Bagan again won the IFA Shield. Through that victory Mohun Bagan is the first Indian club to win IFA Shield after independence. The club also won the Calcutta Football League again by defeating arch rival Kingfisher East Bengal F.C. 
In 1952 Mohun Bagan won the IFA Shield. Three Mohun Bagan players Sailen Manna, M. A. Sattar and Runu Guha Thakurta were selected in the national squad for the Helsinki Olympics of 1952. Sailen Manna was the captain of the team. For both the Olympics of 1948 and 1952, Mohun Bagan's players captained the Indian national football team.
In 1954 the club grabbed the double crown of Calcutta for the first time after winning the IFA Shield and First Division Calcutta Football League and thus also becoming the first club ever to do this. They would also go on to do this again in 1960. In 1977 the club created the history by being the first ever Indian football club to do the triple crown (IFA Shield, Durand Cup, and Rovers Cup) in the same year.
In 1977 Mohun Bagan Club made even more history by playing a friendly match against famous North American Soccer League club New York Cosmos and Pelé. The match which took place at the Eden Gardens had a match attendance of 80,000. The match ended 2-2 and a lot of the Bagan players git a lot of praise by the star packed Cosmos. In the same year Mohun Bagan won the triple crown for the first time - IFA Shield, Durand Cup & Rovers Cup. 
In 1978 Mohun Bagan won the Federation Cup for the first time. The same year Mohun Bagan drew 2-2 with Ararat of USSR in the finals of the IFA shield & went won to be the joint winners of the trophy. The Ararat team boasted of as many as six world cup footballers who were in the team that participated in the world cup in 1978.
In 1998 Mohun Bagan won the triple by winning the IFA Shield, Federation Cup and the National Football League for the first time. In 2002 the football icon of India, Baichung Bhutia came back home from Bury F.C. in England, and Mohun Bagan club officials did not make any mistake to sign him in the squad.
In 2007 Mohun Bagan won the Indian Super Cup by defeating Dempo SC by 4-0.