Background: Increasing evidence has shown benefits of spinal manipulations in patients with patellofemoral pain syndrome (PFPS). There is scarcity regarding medium term effects of spinal manual therapy on outcome measures in PFPS patients. Therefore, the aim of the present study was to compare the effectiveness of local exercise therapy and spinal manual therapy for knee pain, function and maximum voluntary peak force (MVPF) velocity of the quadriceps in PFPS patients. Methods: Forty-three patients with PFPS were randomly assigned to a local exercise or spinal manual therapy group. The local exercise group received six sessions (one session per week) of supervised training of the knee-and hip muscles with mobilization of the patellofemoral joint. The spinal manual therapy group received six interventions (one intervention per week) of high velocity low thrust manipulations at the thoracolumbar region, sacroiliac joint, and/or hip. All patients were also asked to do home exercises. Maximum, minimum and current pain were measured using the visual analogue scale. Function was assessed with the anterior knee pain scale (AKPS) and MPFV was recorded using a Biodex System 3 dynamometer. Patients were assessed before intervention, after 6 weeks of intervention and after 6 weeks of follow-up. Between-group differences at assessments were analysed by way of analysis of covariance with Bonferroni correction. Results: Pain and functionality improved more following spinal manipulative therapy than local exercise therapy. After 6 weeks of intervention the between-group difference (local versus spinal) for maximal pain was 23.4 mm [95% CI: 9.3, 37.6; effect size (ES): 1.04] and − 12.4 [95% CI: − 20.2, − 4.7; ES: 1.00] for the AKPS. At 6 weeks of follow-up the between-group difference for maximal pain was 18.7 mm [95% CI: 1.4, 36.0; ES: 0.68] and − 11.5 [95% CI: − 19.9, − 3.3; ES: − 0.87] for the AKPS. Conclusions: This study suggests that spinal manual therapy is more effective than local exercise therapy in improving pain and function in patients with PFPS in the medium term. We suggest for future research to investigate whether combining local exercise therapy and spinal manual therapy is more effective than either single intervention on its own. This clinical trial study was approved by the Medical Ethics Committee METC Z under registration number NL57207.096. and registered retrospectively in ClinicalTrials.gov PRS with registration ID number NCT04748692 on the 10th of February 2021.