Professional athletes need to maintain certain level of physical fitness level regardless of existence of chronic pain. A training program to maintain the fitness level without aggravating pain should be introduced. Therefore, the purpose of this study was to analyze the effects of a short-term conditioning training for 3 weeks during off-season in elite college soccer players to improve physical fitness level and chronic pain. A total of 53 elite collegiate soccer players were divided in to pain (n=23) and healthy (n=30) groups. A short questionnaire, body composition, physical fitness, isokinetic muscle strength, and anaerobic tests were performed before and after the program. Pain was assessed using the visual analogue scale (VAS). Training program composed of aerobic, functional, anaerobic power, weight training and isokinetic. The program excluded excessively distressing actions such as high jump or sprint. Pre and post comparisons showed significant changes in muscle (%) and fat (%) in the pain group and weight (kg), muscle, and fat in the healthy group. Flexibility (cm) was significantly increased in the pain group and reaction time (msec), balance (sec), and sit up (rep) were significantly improved in the healthy group. Significant improvements were shown in all flexion and extension isokinetic strength in both groups. Significant reductions were shown in the pain group during both resting and training. Results indicate that a short-term exercise intervention improved or maintained muscle strength and physical fitness to the level of healthy soccer players without aggravating chronic pain.