Several techniques have been developed in Drosophila to control gene expression temporally. While some of these techniques are incompatible with existing GAL4 lines, others suffer from side effects on physiology or behavior. Here, we describe a method of post-translational temporal control of gene expression which is compatible with the current library of transgenic reagents. We adopted a strategy to regulate protein degradation by fusing a protein of interest to a destabilizing domain (DD) derived from the Escherichia coli dihydrofolate reductase (ecDHFR). Trimethoprim (TMP), a stabilizing small molecule, binds to DD and blocks degradation of the chimeric protein. With a GFP-DD reporter, we show that this system is effective across different tissues and developmental stages in the fly. Notably, feeding flies with TMP can increase the expression level of GFP-DD up to 34 times in a dosage-dependent and reversible manner without altering the lifespan or behavior of the animal. To broaden the utility of our method, we engineered GAL80-DD flies that can be crossed to the available GAL4 lines to control the temporal pattern of gene expression with TMP. We also developed an inducible recombinase, FLP-DD, for high-efficiency sparse labeling and intersectional lineage analysis. Finally, we demonstrated the utility of the DD system in manipulating neuronal activity of sensory neurons. In summary, we have developed a system to control in vivo gene expression levels with negligible background, large dynamic range, and in a reversible manner, all by feeding a small molecule to Drosophila melanogaster.