Background: World Health Organisation recommends quinine plus clindamycin as first-line treatment of malaria in the first trimester of pregnancy and as a second-line treatment for uncomplicated falciparum malaria when artemisinin-based drug combinations are not available. We compared the efficacy of quinine plus clindamycin with that of artemether-lumefantrine in the treatment of uncomplicated Plasmodium falciparum malaria in children below 5 years of age. Methods: An open-label, phase 3, randomised trial was conducted in western Kenya. Children aged 6-59 months with uncomplicated falciparum malaria were randomly assigned (1:1) via a computer-generated randomization list to receive 3 days of twice a day treatment with either oral quinine (20mg/kg/day) plus clindamycin (20mg/kg/day) or artemether-lumefantrine tablets (artemether 20mg, lumefantrine 120mg). The primary outcome was a PCR-corrected rate of adequate clinical and parasitological response (ACPR) on day 28 in the per-protocol population. Results: A total of 384 children were enrolled and randomised, 192 to quinine plus clindamycin and 192 to artemether-lumefantrine. A total of 353 (92%) children were analysed. The PCR-corrected ACPR rate was 44.0% (80 children) in the quinine plus clindamycin group and 97.1% (166 children) in the artemether-lumefantrine group (treatment difference -53.1%, 95% CI -43.5% to -62.7%). At 72h after starting treatment, 50.3% (94 children) in the quinine plus clindamycin group were still parasitemic compared with 0.5% (1 child) in the artemether-lumefantrine group. Three serious adverse events occurred in the quinine plus clindamycin group. Conclusions: We found no evidence to support the use of quinine plus clindamycin in the treatment of uncomplicated falciparum malaria in children under 5 years of age in Kenya, where artemether-lumefantrine is still effective. Trial Registration: This trial is registered with the Pan-African Clinical Trials Registry, ACTR20129000419241.