The purpose of this study was to investigate differences in the alignment pattern of the collapsed maxillary arch following fixed orthodontic treatment (FOT) in bilateral cleft lip and palate (BCLP) patients according to collapse type. Fifteen BCLP patients were divided into Group 1 (anteroposterior-collapsed arch, n = 7) and Group 2 (transverse-collapsed arch, n = 8) according to maxillary arch shape before FOT. Linear and angular variables of lateral cephalograms and dental models were evaluated before (T1) and after FOT (T2), and statistical analysis was performed. In cephalometric measurements at T1, both the groups exhibited retrusive maxillae, a Class III relationship, and lingual inclination of U1-SN. At T2, significant improvement of U1-SN was observed in both the groups (P < 0.01 in Group 1; P < 0.05 in Group 2). In the model measurements at T1, the inter-second premolar width (IP2W), inter-first molar width (IM1W), and left segmental angle were smaller in Group 2 than in Group 1 (IP2W, P < 0.001; IM1W, P < 0.05; LSA, P < 0.05). From T1 to T2, the arch width increased significantly in Group 2 (inter-canine width, IP1W, IP2W, and IM1W; all P < 0.05), but not in Group 1. Therefore, there were significant differences in ΔIP2W (2.4 mm versus 14.9 mm, P < 0.01) and ΔIM1W (−0.7 mm versus 5.9 mm, P < 0.001) between Groups 1 and 2. In both the groups, the molar depth and right and left segmental angles increased significantly, while the premaxillary rotation angle decreased significantly (molar depth, RSA, LSA, and PMRA; all P < 0.05). The alignment strategy for the maxillary premolar and molar areas should be modified according to arch shape in BCLP patients.