The evidence-based treatment of patellofemoral pain (PFP) suggests that therapeutic exercise (TE) focused on improving muscle strength and motor control be the main conservative treatment. Recent research determined that the success of the TE approach gets improved in the short term by the addition of neuromodulation via radiofrequency diathermy (RFD). As there is no follow up data, the objective of this research is to assess the long-term effects of adding RFD to TE for the pain, function and quality of life of PFP patients. To this aim, a single-blind randomized controlled trial was conducted on 86 participants diagnosed of PFP. Participants who met the selection criteria were randomized and allocated into either a TE group or an RFD + TE group. TE consisted of a 20 min daily supervised exercise protocol for knee and hip muscle strengthening, while RFD consisted of the application of neuromodulation using a radiofrequency on the knee across 10 sessions. Sociodemographic data, knee pain and lower limb function outcomes were collected. The RFD + TE group obtained greater improvements in knee pain ( < 0.001) than the TE group. Knee function showed statistically significant improvements in Kujala ( < 0.05) and LEFS ( < 0.001) in the RFD + TE group in the short and long term. In conclusion, the addition of RFD to TE increases the beneficial effects of TE alone on PFP, effects that remain six months after treatment.