Background: Cleft palate only (CPO) is the second most prevalent cleft type. Both the cleft and palatal scarring may affect craniofacial growth. The aim of this systematic review was to summarize scientific evidence on effect of palatal surgery on craniofacial morphology in CPO. Methods: A search was conducted in PubMed, PMC, WoS, Scopus, Embase, using the keywords: “cleft palate” AND (“craniofacial morphology” OR “cephalometric analysis”) NOT “lip” with inclusion and exclusion criteria ensuring confident, direct comparison between study groups. The quality assessment was performed with Arrive’s scale for radiologic examinations. Results: Of 713 potential articles, 19 were subjected to qualitative analysis and 17 to meta-analysis, which confirmed reduced SNA in unoperated CPO versus non-cleft individuals. No scientific evidence was found directly assessing the effect of surgery on craniofacial morphology. The negative effect of palatal surgery was seen indirectly: in treated CPO versus non-cleft, the size effect of SNA is bigger than in untreated CPO versus non-cleft. A high heterogeneity came from a few non-European publications. Conclusions: CPO is associated with sagittal maxillary deficiency resulting both from the cleft and from primary surgery, disregarding cleft severity in operated CPO patients. Ethnic differences influence craniofacial morphology in CPO. This research received no external funding. Study protocol number in PROSPERO database: CRD42021268957.