There is a paucity of data on paediatric kidney disease in developing countries such as Malawi. Descriptive research on kidney disease is essential to improving patient outcomes. We conducted a cross-sectional study at a tertiary hospital in Malawi from 2012 to 2013. Children under 14 years with proteinuric kidney disease were enrolled from paediatric wards and outpatient clinics at Queen Elizabeth Central Hospital (QECH). Demographic, clinical and laboratory data were collected from patients at enrolment and at 3 months review at which point clinical status and disease outcome were ascertained. Thirty-four (22 male) patients were studied, mean age 8.54 (SD = 3.62 years). Glomerular disease (n = 25, 68%) was the most common presumed renal lesion at presentation. Nephritic syndrome (10) was characterised by a lower baseline complement C3 than nephrotic syndrome (p = 0.0027). Seven (47%) cases of nephrotic syndrome achieved complete remission. Eight (80%) cases of nephritic syndrome improved with supportive therapy. Nineteen (56%) patients presented with clinically significant renal damage with eGFR< 60 ml/min/1.73m2. Six patients presented in chronic kidney disease (CKD) stage 5 of unclear aetiology, five (83%) died. Three (9%) patients had impaired kidney function and obstructive uropathy demonstrated on ultrasound, two recovered after surgery and one died. Eight (24%) patients had acute kidney injury (AKI) due to primary kidney disease, three of these patients progressed to CKD stage G3a. Seven (21%) patients were lost to follow up. Kidney disease is a significant cause of mortality and morbidity in children at QECH. Less than half of Nephrotic syndrome cases achieved complete remission. Mortality is highest in children with CKD of unclear cause. Some patients with AKI secondary to primary renal disease progressed to CKD. Understanding the aetiology of paediatric kidney disease and improving patient outcomes by developing enhanced diagnostic and clinical services are priorities at QECH and within Malawi.