Value of the data •The dataset complements existing resources on the growth cone composition. Lipid and protein time-course profiling analysis of growth cone-enriched and non-growth cone membrane fractions may be of interest to developmental and regenerative neuroscience research. •The dataset can be used to derive information on the growth cone composition throughout the tested period or at the specific developmental time-point. The data can be integrated with other omics approaches. Hypotheses on the specific lipid and/or protein changes and their potential role in growth cone biology may be generated from this dataset and form the basis of functional studies. •The data can be used to create peptide/lipid spectral libraries for targeted proteomic/lipidomic experiments.