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 Caenorhabditis elegans. We use genetic code expansion to incorporate photocaged amino acids into FLP, replacing critical residues in the active site wi