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Background In eastern Uganda, reports suggest that cases of Blackwater Fever (BWF) are on the rise. We summarise the base-line characteristics and routine care available to patients with BWF presenting at two tertiary hospitals in Eastern Uganda prior to the Phase I/II trial on use of paracetamol for acute kidney injury in children with BWF (PARIST; ISRCTN84974248). Methods This was a retrospective descriptive study for the period January – December 2018 for children admitted with a clinical diagnosis of BWF at Mbale and Soroti Regional Referral Hospitals in Eastern Uganda. Data on sociodemographic and clinical characteristics, routine in-patient care and outcomes were abstracted using a customised study proforma and analysed using STATA. Results We obtained 9578 admission records during the study period, of which 1241 (13.0%) were admitted with a diagnosis of BWF. The median age was 60 months (IQR 36–90). Male: female ratio was 1.5:1. More cases of BWF 682/1241 (55.0%) were in children > 5 years compared to 559/1241 (45.0%) ≤ 5 years [95% CI (0.41–0.59); P = 0.0002]. The common symptoms included fever 1109/1241 (89.4%), vomiting 599/1241 (48.3%) and abdominal pain 494/1241 (39.8%). Conversely, the common signs recorded were clinical pallor 742/1241 (59.8%), clinical jaundice 369/1241 (29.7%), fever 332/1241 (26.7%) and prostration 231/1241 (18.6%). In addition, abdominal tenderness was documented in 120/1241 (9.7%), splenomegaly in 122/1241 (9.8%) and hepatomegaly in 86/1241 (6.9%). Case records with BWF were more in the second half of the year with a peak in the months of July and September. 510/1241 (41.1%) were treated with antimalarial drugs mainly parenteral Artesunate 501/510 (98.2%). 660/1241(53.2%) of the patients were managed with antibiotics mainly parenteral ceftriaxone 616/660 (93.3%). There were 426/1241 (34.3%) patients who received blood transfusion during admission. Clinicians used steroid treatment in 388/1241 (31.3%), mainly parenteral hydrocortisone 370/388 (95.4%). Conclusions BWF accounted for 13% paediatric hospital admissions in the region. It was predominant in children > 5 years of age. It typically presents with passing dark urine, fever, abdominal pain, clinical jaundice and pallor. Locally there are no treatment guidelines for BWF. These data provide background data useful for future studies on BWF in the region.