Growth factor-mediated signaling pathways regulate neuronal survival, proliferation, differentiation, and apoptosis. The mitogen-activated protein kinase (MAPK) signaling pathway is a primary signaling cascade downstream of the binding of neurotrophins to their receptors. Evidence suggests that signaling output of the MAPK pathway varies with its temporal kinetics. A quantitative delineation of signaling kinetics is limited due to a lack of tools that allows precise temporal control of the MAPK pathway. The emerging non-neuronal optogenetics, which utilizes light to control intracellular signaling pathways, provides a new modality for spatiotemporal signaling control. We have developed an optogenetic system that allows reversible activation of the MAPK signaling pathway in intact cells and in developing Xenopus laevis embryos. In PC12 neuronal cell lines, light-controlled, intermittent MAPK activity reveals a memory effect in light-induced neurite outgrowth. In Xenopus embryos, developmental stage-specific MAPK activation implies that this pathway can reprogram cell fate after germ layer specification, a crucial time window during which destination of cell fate is set. Our strategy can be generalized to control other kinase pathways with a similar activation mechanism. Results from our research will help resolve intracellular mechanisms of neurotrophin-regulated signal transduction during cell differentiation and embryonic development.