Compensatory increases in net photosynthetic assimilation rates (Anet) following herbivory are well documented in adult rangeland grasses but have not been quantified in bunchgrass seedlings, which may be more sensitive to tissue loss than established plants. To address this, we twice removed 30% and 70% leaf area of seedlings of crested wheatgrass (Agropyron cristatum [L.] Gaertn., var. Hycrest II) and the native bluebunch wheatgrass (Psuedoroegnaria spicata [Pursh] Á. Love, var Anatone) and compared Anet and aboveground and belowground growth of these to unclipped control plants. Compensatory Anet occurred only after the second clipping, roughly 1 month after the first, and was similar in magnitude and duration between species and treatments, ca. 26% higher than control plant Anet for 2 weeks following clipping. Despite similar compensatory Anet between species, increases in Anet were more proportional with increased stomatal conductance to water vapor (gs) in crested wheatgrass. This resulted in higher intrinsic water use efficiency (WUEi = Anet/gs) integrated across the post-clipping recovery period compared with WUEi of bluebunch seedlings, which declined with clipping. Differences in WUEi were attributable to differences in root-to-shoot ratios and root tissue quality (specific root mass; g dry mass · m−2 root area), which were lower in crested wheatgrass. We concluded that compensatory photosynthesis is an important component of seedling herbivory tolerance, and that observed differences in post-herbivory WUEi could help improve management strategies by informing seedling selection criteria to help develop methods aimed at minimizing impacts of herbivory during the seedling stage.