Introduction: There is inconsistent clinical presentation of rare orofacial clefts, and its low number has resulted in most studies on rare craniofacial clefts to be retrospective in nature, with significant amount published as case reports. Objectives: To study the pattern, challenges, and management of rare craniofacial clefts in a Nigerian population. Material and methods: This is a retrospective observational study of patients with rare facial clefts, who visited private health institutions between January 2009 and August 2018. Data retrieved was analyzed using statistical package for social sciences (SPSS), version 16 (SPSS Inc., Chicago, IL, USA). Results: Of the 899 patients who presented with orofacial clefts within the reviewed period, a total of 20 patients had rare facial clefts, with typical to rare craniofacial cleft ratio of 46.3 : 1. The prevalence rate of rare craniofacial cleft was 22.2 per 1,000 cases. Age of patients ranged from 0.04 to 37.00 years, with median age of 3.50 ± 36.96 years. There were 10 males and 10 females, with male to female ratio of 1 : 1. Tessier number 0 had the highest frequency (n = 9, 36.0%), followed by Tessier number 7 (n = 3, 12.0%) and 2 (n = 3, 12.0%). Repair was achieved using local tissue advancement and direct closure techniques under general anesthesia in 10 patients and local anesthesia in 6 patients. Coloboma of the eyelid was the most common abnormality noted. Conclusions: The prevalence of rare craniofacial clefts is low in this environment and Tessier 0 cleft is the commonest type seen. Treatment is generally challenging due to inadequate manpower.