Background. The progressive resistance exercise (PRE) in Parkinson’s disease trial (PRET-PD) showed that PRE improved the motor signs of PD compared to a modified Fitness Counts (mFC) program. It is unclear how long-term exercise affects physical function in these individuals. Objective. To examine the effects of long-term PRE and mFC on physical function outcome measures in individuals with PD. Methods. A preplanned secondary analysis was conducted using data from the 38 patients with idiopathic PD who completed the PRET-PD trial. Participants were randomized into PRE or mFC groups and exercised 2 days/week up to 24 months. Blinded assessors obtained functional outcomes on and off medication at baseline, 6 and 24 months with the Modified Physical Performance Test, 5 times sit to stand test, Functional Reach Test, Timed Up and Go, Berg Balance Scale, 6 minute walk test (6MWT), and 50-ft walking speed (walk speed). Results. The groups did not differ on any physical function measure at 6 or 24 months ( Ps > .1). Across time, all physical function measures improved from baseline to 24 months when tested on medication ( Ps < .0001), except for 6MWT ( P = .068). Off medication results were similar except that the 6MWT was now significant. Conclusions. Twenty-four months of supervised and structured exercise (either PRE or mFC) is effective at improving functional performance outcomes in individuals with moderate PD. Clinicians should strive to include structured and supervised exercise in the long-term plan of care for individuals with PD.