Stade Malien has inherited much of the history of Jeanne d'Arc du Soudan, founded in 1938 by two French-Africans and the missionary Révérend Père Bouvier.

JA du Soudan was one of the most successful clubs of the pre-independence period, winning the AOF Cup in 1953 and 1956 and reaching the finals in 1951 and 1959 (the last played).

Espérance de Bamako was founded in 1958 as a student youth club, overseen by Fernand Diarra and captained by the young Bakary Samaké.

Other famous early players for the Blancs were Yacouba Samabaly, Bakary Samaké, Sama Bass and Coach Oumar Sy.

During the 1968–91 military dictatorship of Moussa Traoré, many fans of Stade Malien felt that the government unfairly favored Djoliba AC.

Heroes of this era include Mamadou Kéita "Capi",[4] Issa Yatassaye, Osumane Farota, Drissa Coulibaly, Abdoulaye Kaloga, Moussa "Gigla" Traoré.

At the end of the 2006–07 season, a group of Stade supporters broke away to form their own football club, taking the "Jeanne d'Arc" name with them.

Their 7 July derby match was postponed to August, and although they beat their rivals, Stade finished the season 9 points behind champions Djoliba.

In the league, their biggest win was a 5–0 defeat of USFAS Bamako on 14 July at home, with scorers Lassana Diallo, Karim Sogoba, Lassine Diarra, and Bakary Coulibaly scoring two.

[10] Despite winning eight of their nine last matches (they lost 1–0 away to JS Centre Salif Keita on 14 August), Djoliba handily took the cup and league double.

While other reasons were given, the removal of the Club Director Mahamadou Samaké at the beginning of September, after eight years at the helm, was reported in the press as a result of this disappointing season.

[14] Earlier in the season, the club brought in two Burkinabé players, goalkeeper Rachid Abdoulaye Compaoré (to supplement national squad keeper Soumaila Diakité who was suspended from CAF play) and striker Moctar Ouédraogo (who has become a starter).

[16] Following a particularly poor result, a group of Stade fans attacked the home of a match official, and incurred a one million FCFA fine from FEMIFOOT.

Standing just nine points off relegation on 10 February, the board sacked three players and manager Cheick Oumar Koné, replacing him with goalkeeping coach and former Malian international Yatouma Diop on an interim basis.

[18] Stade Malien won the Confederation Cup for the year 2009 in a hard-fought battle against the Algerian giant Entente Sétif.

However, in the second leg, which was played on 5 December 2009 before 20–50.000 spectators at Modibo Keita Stadium in the Malian capital, the Bamako-based team stunningly overcame the Algerian side 3–2 on penalties after the regular 90 min.

This conclusive victory of Stade Malien was first of its kind in the history of Malian football as the country had never before won a real continental cup.

Stade Malien and AS Real de Bamako as well as the country's national team, les Aigles du Mali, had been high value continental runner-up in the years of 1964, 1966, and 1972.

[21] In August 2008, he announced he was stepping down nominally to accept a promotion in his business work, it is rumored his resignation had more to do with more than a season of disappointing on field results.

[14] In 2007, the board named three men Honorary Presidents for Life: Dioncounda Samabaly, Mody Sylla, and Amadou Beydi Wane.

They came back to the 2013 Super Cup as champion and as the match ended in a scoreless draw, they lost the penalty shootouts do Djoliba 4–2.