Abstract Background Juvenile-onset systemic lupus erythematosus (jSLE)) is a rare but severe multisystem autoimmune, inflammatory disease that can affect any organ system and cause significant morbidity and mortality. The disease onset occurs before the age of 18, however the peak age of onset is between 12 and 14 years and it affects ∼15–20% of all SLE patients. Patients with disease onset before 5 years of age are very uncommon and may be referred to as early-onset SLE. They commonly present with fever and general malaise, rash and arthritis. In addition, cases of jSLE, tend to have more severe organ manifestations and greater damage at the time of diagnosis as well as a higher incidence of renal, cardiovascular and neuropsychiatric involvement. Compared with adult-onset SLE, it is more aggressive, with higher medication burden including corticosteroids and other immunosuppressive drugs. Method and results This case report reviews the journey of a 5-year-old boy, who developed recurrent skin rashes, fever and generalised lymphadenopathy in his second year of life. After multiple hospital admissions and various investigations at different facilities spanning a year, he was admitted to the paediatric emergency unit at a tertiary hospital on account of an acute infection. On presentation, he was pyrexial. There were hypo- and hyperpigmented lesions extending over his scalp, face and upper arms as well as vasculitic lesions in his palms and soles; lip ulcers, sparse brown hair and multiple, non-tender lymph nodes in the cervical, supraclavicular and axillary regions. Respiratory examination revealed a right lobar pneumonia. Heart rate was 112 bpm and heart sounds were normal, however an echocardiogram showed a moderate pericardial effusion with no signs of tamponade. His abdomen was distended with a non-tender hepatomegaly. There was no synovitis. He was lethargic, but had no focal neurological signs. Laboratory results were as follows: normocytic anaemia (8.5 g/dl); ESR (120 mm/h); deranged transaminases; albumin (32 g/dl); Creatinine (12umol/l); urinalysis was normal, positive antinuclear antibody (1:320); positive double-stranded DNA (1:40); positive anti-smith, anti-Ro and anti-RNP antibodies; low C3, C4. A lymph node biopsy showed reactive changes only, with no evidence of haematological malignancy. The diagnosis of jSLE was confirmed at age 3yrs. The acute illness due to pneumonia was treated with antibiotics. Prednisolone 10 mg, Hydroxychloroquine (HCQ) 80 mg daily, Azathioprine 25 mg daily, calcium supplementation and gastric protection were added to manage the jSLE. He made an initial recovery and was managed in the outpatient clinic for months. However, his illness flared up again around age 4 years when he developed generalized seizures, facial and pedal oedema, low urine output, proteinuria 3+, low albumin (25 g/dl), creatinine (252umol/l) and high urine albumin-creatinine ratio (278.62 mg/mmol) reflecting new renal and CNS involvement. A renal biopsy was not available. He received pulse iv methylprednisolone 250 mg daily for 3 days followed by monthly iv cyclophosphamide therapy 500 mg (NIH Regime) which was discontinued after the 5th cycle due to haemorrhagic cystitis. He eventually continued treatment with mycophenolate mofetil 125 mg daily, HCQ 80 mg daily, Prednisolone 10 mg daily, Nifedipine and Enalapril and a year later, has low activity from the cutaneous, renal and CNS manifestations. There is renal damage (creatinine 180 μmol/l) and hypertension, as well as treatment complications from prednisolone causing bilateral cataracts. Conclusion Early diagnosis of jSLE is still a challenge and a high index of suspicion is required especially in the very young. Severe presentation and aggressive clinical course is associated with tissue damage, as in the case presented. Management is complex and we were challenged by the choice and availability of treatment suitable for the severity of his disease, bearing in mind that damage can occur early especially in a male child. In addition, it is important to consider his young age and long-term exposure to drug toxicity and complications.