BackgroundPeople with patellofemoral pain (PFP) exhibit impaired psychological and pain processing factors (i.e., kinesiophobia, pain catastrophizing and pressure pain thresholds [PPTs]). However, it remains unclear whether these factors have different presentations in women and men with PFP, as well as whether their correlation with clinical outcomes differ according to sex. The aims of this study were to: (1) compare psychological and pain processing factors between women and men with and without patellofemoral pain (PFP); (2) investigate their correlation with clinical outcomes in people with PFP.MethodsThis cross-sectional study included 65 women and 38 men with PFP, 30 women and 30 men without PFP. The psychological and pain processing factors were assessed with the Tampa Scale of Kinesiophobia, Pain Catastrophizing Scale, and PPTs of shoulder and patella measured with an algometer. Clinical outcomes assessed were self-reported pain (Visual Analogue Scale), function (Anterior Knee Pain Scale), physical activity level (Baecke's Questionnaire), and physical performance (Single Leg Hop Test). Generalized linear models (GzLM) and effect sizes [Cohen’sd] were calculated for group comparisons and Spearman's correlation coefficients were calculated to investigate correlations between outcomes.ResultsWomen and men with PFP had higher kinesiophobia (d= .82,p= .001;d= .80,p= .003), pain catastrophizing (d= .84, p < .001;d= 1.27,p< .001), and lower patella PPTs (d= -.85,p= .001;d= -.60,p= .033) than women and men without PFP, respectively. Women with PFP had lower shoulder and patella PPTs than men with PFP (d= -1.24, p < .001;d= -.95,p< .001), but there were no sex differences in those with PFP for psychological factors (p> .05). For women with PFP, kinesiophobia and pain catastrophizing had moderate positive correlations with self-reported pain (rho = .44 and .53,p< .001) and moderate negative correlations with function (rho = -.55 and -.58,p< .001), respectively. For men with PFP, only pain catastrophizing had moderate positive correlations with self-reported pain (rho = .42,p= .009) and moderate negative correlations with function (rho = -.43,p= .007).ConclusionsPsychological and pain processing factors differ between people with and without PFP and between sexes, respectively. Also, correlations between psychological and pain processing factors with clinical outcomes differ among women and men with PFP. These findings should be considered when assessing and managing people with PFP.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12891-023-06513-8.