Acute malnutrition, defined as a weight-for-height Z-score below -2 standard deviations of the WHO growth standards, is prevalent among children in low- and middle-income countries. Our study aimed to identify immediate, underlying, and basic determinants of acute malnutrition among children in Turkana and Samburu, two arid and semi-arid regions in Kenya. Data are from a longitudinal study that recruited children under 3 years of age, with follow-up every 4 months over six waves. Generalized estimating equations were used to assess risk factors of acute malnutrition in this population. Among immediate factors, children who recently experienced diarrhea had 19% and 23% higher odds of acute malnutrition and those who consumed animal-source foods had 12% and 22% lower odds of acute malnutrition in Turkana and Samburu, respectively. Among underlying factors, children in Turkana whose caregivers used alcohol had 32% higher odds of acute malnutrition. Among basic factors, children in Turkana whose caregivers had 3-5 or 6 or more children had 39% and 70% higher odds, whereas those in female-headed households had 34% and 81% higher odds of acute malnutrition in Turkana and Samburu, respectively. Children in Turkana fisherfolk communities had 36% higher odds of acute malnutrition compared with those in urban or peri-urban areas. Key risk factors for acute malnutrition included child diarrhea, caregivers use of alcohol (in Turkana), caregivers number of children, female-headed households, and fisherfolk livelihood (in Turkana), while consuming animal-source foods was associated with lower risk. Interventions should target these intersecting factors to reduce acute malnutrition in these counties.