Uncontrolled photoinitiated radical polymerization is used commercially to create polymer networks across a wide range of chemistries and applications including coatings, 3D printing, fine particles, and biomedicine. Despite this ubiquity, radical polymerization typically creates complex gel microstructures that are difficult to control through molecular chemistry alone, leading to empirical optimization of resin formulations to engineer their properties. In this work, we demonstrate an alternative approach that uses time-modulated photoinitiation as a processing tool to control the kinetic development of gel microstructure. Using poly(ethylene glycol) diacrylate hydrogels as a model system, we demonstrate how controlling the time scales of alternating “light” and “dark” photoexposure provides a route to control the molecular weight distribution of active radical oligomers, thereby controlling the topology and structure of crosslinking centers within the emerging network. Rheological measurements elucidate the impact of this process on gelation kinetics and gel mechanics, whereas small angle X-ray/neutron scattering is used to track the resulting changes in final network structure. The results are rationalized using a detailed kinetic model that predicts the time-evolving molecular weight distribution of crosslinking species within the network. Ultimately, we show that low-frequency cycling of photoexposure produces a population of long, bottlebrush-like crosslinking centers that act as rod-like reinforcements of the hydrogel network, leading to significantly enhanced strain-stiffening, toughness and extensibility. The results demonstrate how time-modulated photocuring provides a simple, general, and chemically-orthogonal route to control network structure and properties of photopolymerized materials.