Unconditional cash transfers (UCTs) are used as a humanitarian intervention to prevent acute malnutrition, despite a lack of evidence about their effectiveness. In Niger, UCT and supplementary feeding are given during the June-September "lean season," although admissions of malnourished children to feeding programmes may rise from March/April. We hypothesised that earlier initiation of the UCT would reduce the prevalence of global acute malnutrition (GAM) in children 6-59 months old in beneficiary households and at population level. We conducted a 2-armed cluster-randomised controlled trial in which the poorest households received either the standard UCT (4 transfers between June and September) or a modified UCT (6 transfers from April); both providing 130,000 FCFA/£144 in total. Eligible individuals (pregnant and lactating women and children 6-<24 months old) in beneficiary households in both arms also received supplementary food between June and September. We collected data in March/April and October/November 2015. The modified UCT plus 4 months supplementary feeding did not reduce the prevalence of GAM compared with the standard UCT plus 4 months supplementary feeding (adjusted odds ratios 1.09 (95% CI [0.77, 1.55], p = 0.630) and 0.93 (95% CI [0.58, 1.49], p = 0.759) among beneficiaries and the population, respectively). More beneficiaries receiving the modified UCT plus supplementary feeding reported adequate food access in April and May (p < 0.001) but there was no difference in endline food security between arms. In both arms and samples, the baseline prevalence of GAM remained elevated at endline (p > 0.05), despite improved food security (p < 0.05), possibly driven by increased fever/malaria in children (p < 0.001). Nonfood related drivers of malnutrition, such as disease, may limit the effectiveness of UCTs plus supplementary feeding to prevent malnutrition in this context. Caution is required in applying the findings of this study to periods of severe food insecurity.