A substantial proportion of the world population is affected by malaria with 241 million malaria cases reported globally. Intermittent Preventive Treatment in pregnancy (IPTp) with Sulfadoxine-Pyrimethamine (SP) is an effective chemotherapy but its utilisation has not been optimised. Few studies focus on young mothers and their experiences regarding the optimal uptake of IPTp-SP. The study design was cross-sectional with data derived from six focus group discussions with mothers aged 15-24 years who had a pregnancy and gave birth to a live baby within the last two years in Kisumu and Migori counties, Kenya. Inductive analysis was used to identify themes and patterns. Young mothers were motivated to take IPTp-SP during pregnancy if they had prior knowledge about SP and its associated benefits and if they were knowledgeable about the consequences of malaria infection during pregnancy. Perceived side effects of SP, lack of awareness of SP as a malaria prevention therapy, lack of knowledge on the benefits of SP, dosage and frequency of uptake, poor communication by health providers towards young mothers, and inconsistent supply of SP at health facilities inhibited young mothers from attaining the recommended 3+ doses of IPTp-SP. There is a need for health literacy programmes that focus on increasing knowledge of IPTp-SP dosage, timing and benefits for both the young pregnant mother and her foetus. Community engagement through dialogue with mentor mothers and male partners will be an important complementary approach in establishing a support system for young women for positive health outcomes including attaining the recommended 3+ doses of IPTp-SP.