Primary ciliary dyskinesia (PCD) is a rare autosomal recessive inherited heterogeneous respiratory disorder. The diagnosis of PCD is challenging and necessitates a multi-test diagnostic approach because there are no gold standard diagnostic tests available to confirm PCD. However, rapid advancement in understanding the molecular genetic basis of PCD has greatly improved PCD diagnosis. Studies have reported that PCD may increase the risk of rheumatoid arthritis, congenital heart disease, severe esophageal diseases, and others. Therefore, the present study aimed to assess the risk of type 1 diabetes mellitus (T1DM) in a genetically confirmed PCD patient. In this case study, an 11-year-old girl with autosinopulmonary infections and her younger brother were diagnosed with PCD. The patient’s DNA was extracted for next-generation exome sequencing. Our analysis of the exome sequencing data revealed the PCD-causing genetic variant p.Glu286del in the RSPH9 gene on chromosome 6p21.1. In addition, the biochemical findings at the time of patient’s admission showed elevated glutamic acid decarboxylase antibodies, HbA1c, and ketone levels, with impaired glucose tolerance, which indicated the presence of T1DM. In conclusion, the clinical features, biochemical reports, and genetic testing confirmed PCD in this patient and the possible association between PCD and T1DM.