Pain in the lower limbs is common in athletes and a limiting factor in performance. Acupuncture has shown positive effects as an analgesic treatment and may potentially be used for pain reduction in runners. This study aimed to analyze the parameters associated with knee pain by correlating strength parameters of the musculature assessed in runners treated with acupuncture. A descriptive longitudinal study was conducted on 34 runners of both sexes aged 20 to 52 years, who presented with knee-related pain from January to June, 2015. Two pain questionnaires and a maximal strength test with electromyographic evaluation of the rectus femoris, vastus lateralis, and medialis muscles were used, and patients were monitored during five follow-up visits after an acupuncture protocol. All participants reported experiencing a decrease in knee pain after treatment. The affected limbs showed an increase in average strength by 34% and 25% compared to the contralateral limb. An increase in the number of motor units recruited for the three muscles was observed in both limbs. In conclusion, the proposed acupuncture protocol was effective in reducing pain symptoms in the knee region of athletes, thus influencing their gain in strength and muscle balance. Level of Evidence IV, Case series.