Growth faltering in children arises from metabolic and endocrine dysfunction driven by complex interactions between poor diet, persistent infections, and immunopathology. Here, we determined the progression of the plasma lipidome among Gambian children (n = 409) and assessed its association with growth faltering during the first 2 years of life using the panel vector autoregression method. We further investigated temporal associations among lipid clusters. We observed that measures of stunting, wasting, and underweight are dynamically associated with each other and that lipid groups containing polyunsaturated fatty acids (PUFAs) and phosphatidylcholines consistently predict future growth outcomes. Linear growth was dynamically associated with the majority of lipids, indicating a higher nutritional demand to improve height compared to weight among growth-restricted children. Our results indicate a critical role for PUFAs and choline in early life dietary interventions to combat the child growth faltering still so prevalent in low-income settings.