After anterior cruciate ligament (ACL) injury, a decrease in muscle strength associated with muscle atrophy is frequently observed. The temporal and spatial effects of reconstructive surgery on muscle atrophy have not been examined in detail. This study aimed to 1) reveal the short and mid-term effects of reconstructive surgery on muscle atrophy, and 2) investigate the differences in the degree of atrophy after ACL reconstruction in the hindlimb muscles. ACL transection with or without reconstructive surgery was performed unilaterally on the knees of rats. Untreated rats were used as controls. At one or four weeks post-surgery, the relative muscle wet weights (wet weight/body weight) of the hindlimb muscles were calculated to assess atrophy. At one week post-surgery, muscle atrophy was induced by ACL transection and further aggravated by reconstructive surgery. Reconstructive surgery facilitated recovery from muscle atrophy in some muscles compared with those without reconstructive surgery (ACL transection alone) at four weeks post-surgery. Muscle atrophy after ACL reconstruction was greater in the rectus femoris and plantar flexors than in the semitendinosus and plantar extensors at one week post-surgery. These results indicate that reconstructive surgery exacerbates muscle atrophy in the first week post-surgery, while facilitating recovery between the first and fourth week post-surgery. After reconstructive surgery, muscle atrophy was observed not only in the quadriceps and hamstrings, but also in the lower leg muscles, suggesting the need for muscle strengthening interventions for the lower leg muscles as well as the quadriceps and hamstrings.