Background: Gait retraining is advocated for the management of patellofemoral pain. This case series examined changes in lower limb variability following 6-weeks of gait retraining in individuals with patellofemoral pain. Methods: Six runners with patellofemoral pain completed a 6-week physiotherapist-guided gait retraining program using minimalist footwear and increased cadence. Approximate entropy joint variability and segment coordination variability were calculated across the entire gait cycle during running at baseline, 6 and 12 weeks and compared using repeated measures analysis of variance and the standardised mean difference (SMD). Findings: Compared to baseline, there were large increases in hip joint transverse plane kinematic variability at 6 (SMD = 1.7) and 12 weeks (SMD = 1.3). Moderate increases in hip joint frontal plane and knee joint sagittal plane kinematic variability were also observed at 6 (SMD = 1.1 & 0.96) and 12 weeks (SMD = 1.1 & 0.89). Knee joint frontal plane and hip joint transverse plane kinetic variability demonstrated large increases from baseline at 6 (SMD = 1.3 & 0.9) and 12 weeks (SMD = 0.9 & 1.0). There was no main effect of time for segment coordination variability. All participants had clinically meaningful improvements in pain (visual analogue change score > 20 mm). Interpretation: Gait retraining increased joint kinematic and kinetic variability in those with patellofemoral pain and these changes persisted over 12 weeks. Increased variability was observed in joint kinematics and kinetics known to influence patellofemoral joint stress, which may vary patellofemoral joint loading patterns and partly explain the clinical effect.