In all land plants, the outer surface of aerial parts is covered by the cuticle, a complex lipid layer that constitutes a barrier against damage caused by environmental factors and provides protection against nonstomatal water loss. We show in this study that both cuticle deposition and cuticle-dependent leaf permeability during the juvenile phase of plant development are controlled by the maize (Zea mays) transcription factor ZmFUSED LEAVES 1 (FDL1)/MYB94. Biochemical analysis showed altered cutin and wax biosynthesis and deposition in fdl1-1 mutant seedlings at the coleoptile stage. Among cutin compounds, -hydroxy fatty acids and polyhydroxy-fatty acids were specifically affected, while the reduction of epicuticular waxes was mainly observed in primary long chain alcohols and, to a minor extent, in long-chain wax esters. Transcriptome analysis allowed the identification of candidate genes involved in lipid metabolism and the assembly of a proposed pathway for cuticle biosynthesis in maize. Lack of ZmFDL1/MYB94 affects the expression of genes located in different modules of the pathway, and we highlighted the correspondence between gene transcriptional variations and biochemical defects. We observed a decrease in cuticle-dependent leaf permeability in maize seedlings exposed to drought as well as abscisic acid treatment, which implies coordinated changes in the transcript levels of ZmFDL1/MYB94 and associated genes. Overall, our results suggest that the response to water stress implies the activation of wax biosynthesis and the involvement of both ZmFDL1/MYB94 and abscisic acid regulatory pathways.