Scrub typhus is a leading cause of treatable febrile illness. It can produce complications and dysfunction of multiple organs in children and is associated with considerable mortality. We attempted to perform a systematic review of original articles published between 1990 to 2020 based on certain selection criteria to estimate the case fatality risk of this disease in children. We addressed the pattern of complications of this disease with its impact on mortality We calculated pooled prevalence with a random effects model (restricted maximum likelihood method) that assumed varying effect sizes between studies using R statistical software. We reported the case fatality rate and its 95% confidence intervals (CIs) in the pooled analysis. Thirty-seven articles with a total of 3329 children were identified for inclusion. The case fatality rate was 1.1% (CI 0.05 to 2, I2=58% and prediction interval 0–6%). The mortality rate showed a declining trend over the last 5 y. Hepatitis (30.68% [95% CI 18.52 to 44.38]) remains the most common complication, followed by shock (14.45% [95% CI 7.71 to 22.85]), pneumonia (14.71% [95% CI 9.76 to 20.48]), acute kidney injury (13.72% [95% CI 8.49 to 19.97]) and meningitis/meningoencephalitis (11.57% [95% CI 7.83 to 15.92]). Multi-organ dysfunction syndrome was the main contributor to mortality.