Our previous study indicates that Drosophila Flightless-1 controls lipid metabolism, and that there is accumulation of triglycerides in flightless-1 (fliI)-mutant flies, where this mutation triggers metabolic stress and an obesity phenotype. Here, with the aim to characterize the function of FliI in metabolism, we analyzed the gene expression and levels of metabolites in fliI-mutant flies. The levels of enzymes related to glycolysis, lipogenesis, and the pentose phosphate pathway increased in fliI mutants; this result is consistent with the levels of metabolites corresponding to a metabolic pathway. Moreover, high-throughput RNA sequencing revealed that Drosophila FliI regulates the expression of genes related to biological processes including chromosome organization, carbohydrate metabolism, and immune reactions. These results showed that Drosophila FliI regulates expression of metabolic genes, and dysregulation of the transcription controlled by FliI gives rise to metabolic stress and to problems in Drosophila development and physiology.