Primary ciliary dyskinesia (PCD) is a rare autosomal recessive genetic disorder. It is caused by a defect in the action of the cilia lining multiple organs of the body, including the lungs, the sinuses, hepatobiliary and reproductive organs. In general, the estimated prevalence of this condition is one in 15,000-20,000 individuals. It is characterized by the triad of chronic sinusitis, bronchiectasis, and situs inversus, which occurs in 50% of the cases. It can be associated with other diseases too. Genetic studies can aid in confirming the diagnosis of this condition. A high degree of suspicion about PCD among pediatricians, neonatologists, otorhinolaryngologists, and pulmonologists is essential to make early referrals of patients before they develop irreversible lung damage. Hence, early diagnosis and appropriate treatment are very important. Multicenter collaborations might improve the quality of treatment and patient outcomes. Here, we discuss a case of PCD with a unique association with type IIIb jejunal atresia, and developmental delay secondary to vitamin B12 deficiency. Moreover, the patient was found to have a novel DNAH9 gene mutation in a compound heterozygous state. This is the first case of this rare disease to be reported from Bahrain. This case report is also associated with an extensive literature review.