Focal segmental glomerulosclerosis (FSGS) represents one of the most common etiologies of nephrotic syndrome. In 10% to 20% of cases, it is associated with steroid resistance and has the potential to progress to kidney failure. Compound heterozygote or homozygote mutations in the NUP93 gene have been associated with FSGS-related nephrotic syndrome. To the best of our knowledge, no case of NUP93 related FSGS has presented in the literature with associated ophthalmological anomaly. In this report, we present the case of a 25-year-old White patient who presented with rapidly progressive chronic kidney disease, congenital bilateral optic nerve atrophy and steroid-resistant nephrotic syndrome. Kidney biopsy showed FSGS with more than 80% foot process effacement on electronic microscopy. Genetic testing by means of whole exome sequencing later showed the presence of biallelic class 4, likely pathogenic variants in the NUP93 gene. Although we cannot exclude another cause, such as a genetic defect outside the genomic regions screened by our exome analyses, for the bilateral optic atrophy observed in our patient, this suggests that this association is not coincidental. Our case report highlights the importance of genetic testing in cases of steroid-resistant nephrotic syndrome that present with syndromic congenital features.