Forces acting on aggregates depend on their properties, such as size and structure. Breakage rate, stable size, and structure of fractal aggregates in multiphase flows are strongly related to the imposed hydrodynamic forces. While these forces are prevalently viscous for finite Reynolds number conditions, flow inertia cannot be ignored, thereby requiring one to fully resolve the Navier–Stokes equations. To highlight the effect of flow inertia on aggregate evolution, numerical investigation of aggregate evolution in simple shear flow at the finite Reynolds number is conducted. The evolution of aggregates exposed to shear flow is tracked over time. Particle coupling with the flow is resolved with an immersed boundary method, and flow dynamics are solved using a lattice Boltzmann method. Particle dynamics are tracked by a discrete element method, accounting for interactions between primary particles composing the aggregates. Over the range of aggregate-scale Reynolds numbers tested, the breakage rate appears to be governed by the combined effect of momentum diffusion and the ratio of particle interaction forces to the hydrodynamic forces. For higher shear stresses, even when no stable size exists, breakage is not instantaneous because of momentum diffusion kinetics. Simulations with particle interaction forces scaled with the viscous drag, to isolate the effect of finite Reynolds hydrodynamics on aggregate evolution, show that flow inertia at such moderate aggregate Reynolds numbers has no impact on the morphology of nonbreaking aggregates but significantly favors breakage probability. This is a first-of-its-kind study that establishes the role of flow inertia in aggregate evolution. The findings present a novel perspective into breakage kinetics for systems in low but finite Reynolds number conditions.