<span class="paragraphSection"><div class="boxTitle">Abstract</div>The ability to precisely control gene expression is fundamental to studying biological processes. Using site-specific recombinases such as FLP, gene expression can be controlled, albeit with limited spatio-temporal precision. We develop a photocaged FLP recombinase, which can be precisely controlled using light, and we demonstrate its efficacy in <span style="font-style: italic;">Caenorhabditis elegans</span>. We use genetic code expansion to incorporate photocaged amino acids into FLP, replacing critical residues in the active site with their photocaged counterparts. Photocaged FLP displays no detectable background activity, and brief illumination can be used to activate FLP with near 100% efficiency. We show that photocaged FLP can be activated by light between 365 and 435 nm, and that it is not activated by light above 450 nm, making it fully compatible with wavelengths commonly used for imaging and optogenetics. Furthermore, we demonstrate that photocaged FLP can be used to switch on expression of target genes in individual cells within the animal using a standard 405 nm microscope-mounted laser to deliver the activating light. Activation by laser requires illumination times of &lt;10 ms per cell. Thus, we have developed a straightforward and efficient tool to precisely control gene expression in the multicellular organism <span style="font-style: italic;">C. elegans</span>.</span>