Abstract Background The effect of hyperalgesia on functionality remains uncertain for individuals with knee osteoarthritis (KOA). This study aimed examine the clinical measures and hyperalgesia’s effect on muscle activity, knee range of motion (ROM) and postural control during the single-leg mini squat (SLMS) in individuals with KOA, determining the correlation between variables. Methods In this cross-sectional study, 60 individuals, 30 healthy (HG, 57.4 ± 6.86 years), and 30 with mild to moderate KOA (KOAG, 59.4 ± 5.46 years) were evaluated by the visual analog scale (VAS), Western Ontario and McMaster Universities Index (WOMAC), and the pressure pain threshold (PPT) in subcutaneous, myotomal, and sclerotomal structures. Muscle activity, knee ROM and postural control were assessed during a SLMS. The analyses were performed in the two phases of the SLMS. Phase 1 - during descending movement (eccentric contraction), Phase 2 - during ascending movement (concentric contraction). Analysis of covariance was applied for each variable separately, using weight as a co-variable. We used Spearman’s test for determining the correlation. Results There was no difference between groups for age, height, and postural control (p > 0.059), but KOAG presented the highest values for VAS and WOMAC (p = 0.000). In addition, EMG activity was higher in KOAG for gastrocnemius medialis and tibialis anterior muscles during phase 1 (p 0.507). Conclusion Hyperalgesia affects the functionality during a single-limb mini squat. There is an important correlation between hyperalgesia and muscle activity, postural control, and clinical measures in individuals with KOA.