The expression of Major Histocompatibility Complex (MHC) molecule is essential for homeostasis of the immune system. Tissue-specific expression of MHC-II is regulated at the level of transcription. The master regulator for transcription of the MHC-II gene is CIITA. Homozygous mutations affecting the CIITA gene results in bare lymphocyte syndrome type-II. The clinical manifestations of heterozygous mutations are not well reported. Hence, this case report aims to provide more insight into the clinical features associated with heterozygous mutations of CIITA. We report a 5-year-old child who had presented with recurrent infections in infancy and systemic lupus erythematosus (SLE) in toddler age.