Acute kidney injury (AKI) occurs in about 1% of cases of malaria; however, in these cases, the mortality rate can be as high as 45%. Thrombotic microangiopathy (TMA) as a cause of AKI in malaria is rare with only a handful cases documented in literature so far. Alternate complement pathway (ACP) dysregulation as a major mechanism of injury in the development of thrombotic microangiopathies is well known. It is proposed that patients with preexisting defects in ACP are usually clinically silent, until stress condition such as infections help manifest them. Herein, we describe the presence of two complement factor H (CFH) variants in an 8-year-old female with vivax malaria associated TMA. The complement workup confirmed dysregulated ACP and revealed two single-nucleotide polymorphisms in CFH gene, i.e. exon-7 rs1061147 (p.Ala243Ala) and exon-9 rs1061170 (p.His402Tyr) which predisposed this patient to develop TMA precipitated by vivax malaria.