This study aimed at assessing changes in condylar position (CP) in growing patients with unilateral posterior crossbite (UPC) undergoing rapid maxillary expansion (RME) followed by fixed orthodontic treatment (FOT) (experimental-group); and growing patients without posterior crossbite (PC) treated with FOT alone (control-group). Cone beam computed tomography (CBCT) images were obtained before treatment (T0), 6months after RME (T1) and after FOT (T2) for the experimental-group (n = 19); and at T0 and T2 for the control-group (n = 22). Condylar position-related measurements including the anterior joint space (AJS), superior joint space (SJS), posterior joint space (PJS), lateral position of condyle (LC) and condylar angle (CA) were measured. Non-parametric tests were used. On the crossbite side, significant increases were found in LC (P = 0.039) and CA (P = 0.007), and on the non-crossbite side significant increases were observed in SJS (P = 0.027) and LC (P = 0.001) between T0, T1 and T2 in patients with UPC. On the right and left sides in the control-group, significant increases were identified in LC (P < 0.001 and P = 0.012, respectively) between T0 and T2. In growing patients with UPC, RME followed by FOT is associated with significant changes in CP-related measurements.