Background Atypical hemolytic uremic syndrome (aHUS) is a severe thrombotic microangiopathy predominantly affecting the kidneys, often associated with complement dysregulation. This study is aimed to analyze the clinical characteristics, treatment outcomes, and long-term implications of aHUS in a resource-limited setting. Materials and Methods A retrospective observational study conducted at an institute between January 2016 and December 2022 included all patients with aHUS, excluding secondary causes and renal transplant recipients. Demographic profiles, clinical features, laboratory parameters, treatment modalities (immunosuppression and plasma exchange), and outcomes were collected. Anticomplement Factor H (anti-CFH) antibody, complement levels, and genetic mutation analysis were performed to ascertain etiological factors. The patient and renal outcomes of anti-CFH positive and negative patients on long-term follow-up were compared. Results Fifty-seven patients (mean age: 12.5 ± 4.9 years; 63% males) were analyzed. Among them, 33 (57.9%) tested positive for anti-CFH antibodies and eight presented postpartum. Initial remission was achieved in 42 (73.6%) patients, with 13 (22.8%) partial and 29 (50.9%) complete remission. The median follow-up duration was 24 months [interquartile range (IQR) 8.5–84]; 12 (21%) patients died, with two deaths during the index admission, six among nonresponders, and 4 among responders. Dialysis-free renal survival was superior in anti-CFH seropositive patients (81.2%) compared to seronegative counterparts (55.9%), while patient survival was statistically similar between the two groups. Elevated anti-CFH titers (>4000 AU/ml), age ≥16 years, female gender, and seizures predicted nonresponsiveness. Conclusion Anti-CFH antibody associated aHUS had better kidney outcomes than the seronegative counterparts. In resource limited settings, a combination of plasma exchange and immunosuppression showed promising results in the short and long term.