In 1984, central defender Monem Munna was exceptional during the clubs first year at the top-flight, earning them a place in the Super Eight, who fought for the league title.

Muktijoddha became the target of many angry local fans of the much more popular clubs and were also victims of poor refereeing decisions during the course of the season.

Although the league failure, Muktijoddha started to build a team for the future and, the following years saw the club spend a hefty sum of money on established domestic players, earning them huge success in the process.

Nakib scored 57 Premier Division goals during the club's rise to prominence at the end of the 20th century, making him their all-time top scorer.

The players included: Mohammed Mohsin, Arun Bikash Dewan, Saiful Bari Titu, Jewel Rana, Ataur Rahman, Masud Rana, Mamun Joarder, Barun Bikash Dewan, Rizvi Karim Rumi, Rakib Hossain, Imtiaz Ahmed Nakib, Mizanur Rahman, Arman Mia, Kazi Mizanur Rahman, Parimal Chandra Pandit, while the three guests players were Satyajit Das Rupu, Arif Hossain Moon and Shahidul Ahmed Ranjan.

Muktijoddha manager Kazi Salahuddin also took charge of the team as they played their first game against India, striker Nakib scored both goals in a 2–4 defeat.

In the second game Mizanur Rahman Mizan scored the lone goal as the club managed to defeat Yemen, nevertheless, they were unable to move past the group stages.

Muktijoddha made their debut in Asia during the 1999-2000 Asian Club Champions league first round, after winning their first Premier Division title in 1998.

On 20 April 2004, the club's striker Saifur Rahman Moni became the first Bangladeshi player to score in the AFC Cup, during a 3–2 defeat against Al Sha'ab Ibb from Yemen.

[15] On 27 March 2007, Alfaz Ahmed netted the first hat-trick in BPL history to give Muktijoddha a 4–1 victory over Rahmatganj MFS.

[21] After spending the previous few years struggling with paying player wages, the club's higher-ups had decided not to participate in the 2021 Bangladesh Premier League citing to a lack of finance.

Club captain Yusuke Kato, sought financial help from the Japanese community and businessmen in a video that was posted on his Facebook profile.

[24] The donations allowed the club to take part in the Bangladesh Premier League and they ended the season finishing in tenth place out of 13 teams which was safe from relegation.