Objectives: Inactivity in individuals with spinal cord injury (SCI) results in low physical fitness, cardiopulmonary endurance and poor quality of life. Sports participation is known to enhance physical fitness. Therefore, the present study evaluated effect of a structured, 12-week MGM Sports Intervention for Sports Intervention Program for SCI (SPISI) on physical fitness and throw-ball performance in individuals with SCI. Materials and Methods: The study was conducted at MGM School of Physiotherapy and Spinal Cord Injury Rehabilitation centre in Navi Mumbai, India. Following ethical approval, 15 individuals with SCI (80% males and 20% females mean age 33.1 ± 7.2 years) were recruited. Upper-extremity explosive power (medicine-ball-throw), agility (t-test), cardiorespiratory endurance (incremental shuttle wheelchair propulsion test) and ball-throwing capacity (maximal-pass test) were evaluated pre- and post-12-week sports intervention programme (SPISI). The protocol involved strength training of upper extremity training at 50% 1 repetition maximum and participation in throw-ball sport. Results: Following training, increase in upper extremity explosive power (11%), cardiopulmonary endurance (5%), agility (8%) and ball-throwing capacity in distance (7%) (P < 0.05) was observed. The large effect size was observed for sports performance (maximal-pass test distance-Cohen’s d 1.261), moderate for cardiorespiratory endurance (incremental wheelchair propulsion test distance Cohen’s d 0.517) and upper extremity explosive power (medicine-ball throw distance 0.593). Increment in all outcome variables was greater than minimal clinically important difference. Conclusion: Sports intervention programme (SPISI) for 12 weeks brought about minimal clinically important difference in upper-extremity explosive power, agility, cardiorespiratory endurance and sport-specific performance and should be included as an integral component of rehabilitation of individuals with SCI.