46,XY complete gonadal dysgenesis (Swyer syndrome) is a rare cause of disorder of sexual development. This syndrome is caused by a defect in the determination of sex during embryogenesis and is characterised with female external genitalia, normal or rudimentary uterus, and streak gonads, despite the presence of the 46,XY karyotype. Most of the studied cases presented with leak of secondary sex characteristics and primary amenorrhea during adolescence. Laboratory findings reveal hypergonadotropic hypogonadism. Herein we present the case of a female with a 46,XY karyotype who was admitted with delayed puberty and detected to have a microdeletion in the SRY gene and diagnosed to have Swyer syndrome. We highlight the importance of karyotype analysis in patients with delayed puberty and primary amenorrhea. Once the diagnosis of 46,XY complete gonadal dysgenesis is established, early laparoscopic removal of the dysgenetic gonads is crucial to prevent the development of gonadal malignancy.