Infantile-onset multisystem neurologic, endocrine, and pancreatic disease (IMNEPD) is a rare autosomal recessive multisystemic disease with a prevalence of 1/1 000 000. The wide spectrum of symptoms and associated diseases makes the diagnosis of this disease particularly challenging. Here, we report a 12-year-old Bahraini male who presented with the core clinical features of IMNEPD including intellectual disability, global developmental delay, sensorineural hearing loss, endocrine dysfunction, and exocrine pancreatic insufficiency. The diagnosis was confirmed by genetic testing using whole exome sequencing. This is the first reported case of IMNEPD from Bahrain and was found to have a novel homozygous peptidyl-tRNA hydrolase 2 (PTRH2) gene mutation (NM_001015509.2: c.370del p.(Glu124Lysfs*4)). Moreover, we conducted an extensive literature review with an emphasis on the variable clinical spectrum and genotypes of previously reported patients in comparison to our case.