Adolescents with COVID-19 and subsequent multisystem inflammatory injury share key features with Kawasaki disease and toxic shock syndrome. As referenced in a United Nations WHO brief from May 2020, findings from North America and Europe drew notice to an acute illness accompanied by severe, diffuse hyperinflammation leading to multiorgan failure. While females diagnosed with COVID-19 generally have more favorable outcomes than males, this protective effect is negated by any low/absent estrogen state. Our research focuses on secondary amenorrhea from pre-adulthood ovarian insufficiency where RUNX2, SALL1 and SAMD9 variants were identified by exon sequencing in a healthy, phenotypically normal 46,XX adolescent. Against this background, COVID-19 infection occurred necessitating hospital admission where multisystem inflammatory syndrome in children (MIS-C) was diagnosed. Although renal function was compromised secondary to COVID-19 infection, this damage was transient and apparently reversed by angiotensin-converting enzyme inhibitor plus transdermal estrogen replacement therapy. This research is the first to study the intersection of multigene variants, ovarian insufficiency, COVID-19, and acute kidney injury as a component of MIS-C. The background transition from adolescence to adulthood is also considered, where successful recovery of renal function was attained using combined enalapril and supplemental estrogen.