Time-dependent surface chemistry and the resulting profile evolution have been studied numerically during pulsed plasma etching of Si in low-pressure, high-density Cl-2 plasmas, to gain an understanding of the effects of surface chemistry on the etch anisotropy and microscopic uniformity achieved with pulsed operation. The time-dependent behavior of surface chlorination and the ion-enhanced desorption of neutral Cl atoms adsorbed, as well as reaction products SiClx from the surface being etched, was calculated in pulsed operation with a simple model based on Langmuir adsorption kinetics. The etched profile evolution was then simulated for infinitely long trenches of different widths, taking into account the transport of ions and neutrals in microstructural features. The numerical results indicated that the chlorinated surface coverage depended strongly on the pulse period as well as on the duty ratio, owing to a competition between adsorption and desorption of neutral reactants on the surface during the pulse period. Correspondingly, the etch anisotropy and microscopic uniformity was significantly improved with pulsed operation by optimizing the pulse conditions to increase the surface coverage at the bottom of the microstructural features.