Post-operative outcomes after simultaneous bilateral total knee arthroplasty in 115 patients randomly assigned to two rehabilitation protocols were compared. The traditional-protocol group performed a series of exercises on one leg and then repeated the same sequence on the other leg. The alternate-protocol group performed the same exercises, but alternated between legs with each individual repetition. Symptoms and function were assessed pre-operatively and at 1, 3, 6 and 12 months post-operatively. The alternate-protocol group had lower visual analogue pain scale scores in the early post-operative period, as well as higher Knee Society Scores and SF-12 physical and mental health summary scores after 1 and 3 months compared with the traditional-protocol group, but there were no differences between the two groups from 6 months post-operatively. There were no significant differences between the groups in terms of range of knee motion or incidence of deep vein thrombosis. The alternate-protocol for rehabilitation resulted in an early return to function and decreased pain levels following simultaneous bilateral total knee arthroplasty and was associated with the potential to produce more positive emotional states and earlier functional independence.