The aims of this retrospective longitudinal study were to present the incidence of external apical root resorption (EARR) in the maxillary anterior teeth of patients with complete unilateral cleft lip and palate (CUCLP) and to evaluate the influence of orthodontic treatment variables on the development of EARR. Forty-one patients with CUCLP participated in the study. Orthopantomograms (OPGs), taken before (T2) treatment with multiband orthodontic appliances (MBA), and periapical radiographs (PAs) of the maxillary anterior teeth taken at the end (T3) of orthodontic treatment (OT) were assessed for EARR. The incidence of EARR at T3 (97.6%) was considerably higher than at T2 (51.2%). Central incisors and canines on the cleft side showed a significantly higher score (p < 0.01, p < 0.05 respectively) of EARR in comparison to the same group of teeth on the non-cleft side. Preexisting EARR and abnormal root morphology were identified as predisposing factors for EARR. Patients with CUCLP treated with MBA have higher incidence of EARR on the maxillary anterior teeth of the cleft side. Severe EARR is rather rare but more often seen on central incisors of the cleft side. As most of the patients with cleft lip and palate undergo a challenging and long-term OT with MBA, it is of importance to identify the predisposing factors related to the special anatomical features of the bone and teeth located in the cleft area, as well as the special OT needs of these patients.