Background/Aims Muscle imbalance in patella stabilisers leads to patellar lateral glide and can cause patellofemoral pain syndrome. This study investigated the effect of progressive strengthening exercises of the vastus medialis oblique on pain and patellar alignment in patients with patellofemoral pain syndrome and patellar lateral glide. Methods A double-blind, randomised controlled trial was conducted with 40 individuals with patellofemoral pain syndrome with patellar lateral glide aged 20–40 years. The study group received vastus medialis oblique-specific strengthening exercises and routine physiotherapy treatment, and the control group received routine physiotherapy treatment only (stretching exercises, gluteal and quadriceps isometric exercises and conventional transcutaneous electrical nerve stimulation). Participants performed these exercises three times a week for 8 weeks. Pain intensity was measured before and after the intervention using a visual analogue scale and patellar alignment was measured using ultrasonographic parameters, including the trochlear angle, patella offset angle and distance between patellar tip and trochlear groove. Results In the between-groups comparison, there was a significant decrease in pain intensity in both the study and control groups, although the study group had a greater decrease (study group before intervention: 71.15 ± 1.54, study group after intervention: 22.21 ± 0.35, P=0.001); control group before intervention: 70.09 ± 1.22, control group after intervention: 31.82 ± 0.36 (P=0.001)) and patella offset angle (in the study group compared to the control group after 8 weeks of intervention. In within-groups comparison, a significant decrease of the patella offset angle in the study group was observed (before intervention: 16.2 ± 1.53; after intervention: 13.2 ± 1.87, P=0.001). No significant differences were found for the other parameters. Conclusions Specific strengthening of the vastus medialis oblique muscle in patients with patellofemoral pain syndrome and patellar lateral glide can lead to pain reduction and improvement of patellar alignment to correct lateralisation. This change may delay the process of patellofemoral joint degeneration. Including vastus medialis oblique-specific strengthening exercises in standard physiotherapy treatments may help to reduce pain levels in people with patellofemoral pain syndrome. Implications for practice Investigating the main cause of patellofemoral pain syndrome could have an essential role in the rehabilitation treatment of patients.