Subroto Mukerjee conceived the idea in 1958 when he was the Chief of the Air Staff. Subroto Mukerjee Sports Education Society was formed in 1960 after his untimely death in Tokyo. The first tournament was held in 1960, with participation of about 50 school teams. The number of schools participating increased over the years. Since 1998, the tournament is played in two age groups, sub-Junior (under 14 years) and Junior (under 17 years).
Preliminary inter-school tournaments are held in every state of India starting from Sub-division, district and division level culminating in the inter-school finals at the national level. The school teams, winning the state inter-school championships are then invited to participate in the main Subroto Mukerjee Cup Tournament at Delhi.
The tournament is on "Knock-out/League" system and is played in accordance with laws and rules relating to Football Association and as accepted and interpreted by the All India Football Federation (AIFF). The duration of the game has been reduced to 30 minutes each half with an interval of 5 minutes. In the event of a draw, extra time of 7 minutes each half with one minute's interval is allowed. If a match ends in a draw even after extra time the Tournament Committee may direct that the game be decided by enforcing the Tie Breaker Rule.
The foundation has still the Chief of the Air Staff of India as its President.
Cash prizes of Rs. 3,00,000/- and Rs. 1,50,000/- are awarded to the winners and runners-up in the junior category, respectively; cash prizes of Rs. 2,00,000/- and Rs. 1,00,000/- are awarded to the winners and runner-up teams in the sub-junior category. Also, there are awards for titles such as "Best Player" and "Most Promising Player" and they are separately awarded with gearless scooters in each group. All the players of the final two teams in both groups are awarded with a blazer, a tie & a Sports Kit. Cash prizes of Rs. 50,000/- and Rs. 30,000/- are awarded to the winners and runners-up in the Girls junior group.Quarter Finalists are awarded with Rs. 30,000/- and Rs. 20,000/- in the boys Junior and Sub-junior categories respectively. Semi Finalists are awarded with Rs. 50,000/- and Rs. 40,000/- in the boys Junior and Sub-junior categories respectively. Semi Finalists of Girls (U-17) category are awarded with Rs. 10,000/- each. Other cash awards are Best Player Rs. 25,000/-, Best Goal Keeper Rs. 20,000/-, Best Coach Rs. 25,000/-, Best player (Girls) Rs. 7,500/-, Best Goal Keeper (Girls) Rs. 7,500/-.Fair Play Trophy along with cash award of Rs. 10,000/- in each category.