Background Gender dysphoria is treated with gender affirmation surgery (GAS) for assigned male at birth (AMAB) individuals. This study aimed to evaluate the postoperative anatomical changes in AMAB individuals who underwent GAS using magnetic resonance imaging (MRI) and to compare it with cis-females, thereby assessing the efficacy of the surgical technique in achieving pelvic anatomy similar to cis-females. Methodology This was a prospective observational study done in a tertiary care hospital. AMAB individuals who underwent gender affirmation genital surgery using single-stage solely penile skin inversion vaginoplasty were included after informed consent and approval by the Institutional Human Ethics Committee. Patients with complications such as deep space surgical site infection (SSI) and neo-vaginal prolapse were excluded. All the study participants were advised a vaginal self-dilatation regimen, reviewed three months after the surgery, and subjected to an MRI of the pelvis with a vaginal tutor. Parameters such as neo-vaginal depth, alpha (α) angle, rectovaginal thickness, and remnant of corpora cavernosa were measured and compared with cis-female parameters measured from images in the archives from the Department of Radiology. Result A total of 21 patients were included in the study, with a mean age of 27±4.7. Between the study group and cis-females, no significant difference was seen in vaginal depth, and cis-females had significantly higher values in other parameters. There was a significant difference between the subgroups, i.e., defaulters and non-defaulters in soft tissue parameters such as vaginal depth (p=0.001), αangle (p=0.002), and rectovaginal thickness (p=0.002) with the non-defaulter patients having higher values. Conclusion Single-stage penile skin inversion vaginoplasty is capable of producing anatomical parameters, importantly neo-vaginal depth, which is fairly comparable with cis-female, as evident in the non-defaulter subgroup patients. Proper compliance with the vaginal dilatation regimen plays a significant role in the maintenance of soft tissue pelvic anatomical parameters.