Structural abnormalities of the foot may cause abnormal subtalar joint compensatory motion in order to attain normal function of the lower extremity during gait although studies have not been conclusive. Current conflict in the literature may be related to the differing measures focused on the varying protocols and also the absence of a control group in some studies. This study investigated the rearfoot posture including Subtalar Joint Neutral Position (STJN) and Relaxed Calcaneal Standing (RCS) measurements in patellofemoral pain syndrome (PFPS) and healthy subjects. The angle of STJN during non-weight bearing position and the two dimensional (2D) rearfoot RCS posture was measured using a goniometer in 14 healthy females and 13 females with PFPS. The RCS posture was also measured three dimensionally (3D) by attaching external markers to a tibia shell and the calcaneus and videoing with a four-camera three-dimensional motion analysis system. A one way ANOVA was used to assess the differences between the groups. The 2D and 3D RCS were significantly different between the groups (p ≤ 0.001) with mean -0.23° ± 1.35° , 2.52° ± 3.11° for the control group and 2.35° ± 1.4°, 7.02° ± 3.33° for the clinical group respectively. STJN showed a slight rearfoot varus (although significant p = 0.04) in PFPS (-2.20° ± 1.51° ) compared to the control group (-1.00° ± 1.36°). Negative values indicated inversion and positive values indicated eversion. The 2D and 3D RCS showed a significantly more everted posture of the rearfoot for the PFPS group. Subtalar joint varus may contribute to the increased eversion during relaxed standing in the PFPS group. Rearfoot measurements may be an important addition to other clinical measurements taken to explore the underlying aetiology of subjects with PFPS.