Herbivorous reef fishes are critically important for maintaining the health and resilience of coral reefs. In the Egyptian Gulf of Aqaba (GoA), many of these herbivores are important fishery targets and little is known about their population size structure and biomass patterns. Here, we conduct a large-scale (~250 km of coastline) assessment of the status of herbivorous fish populations along a fishing pressure gradient at 30 sites and eight regions in the GoA. These regions are subjected to three levels of fishing and protection, ranging from almost no fishing (No take, NT), and moderately fished (via Gear restriction, GR) to heavily fished (Open access, OA). We found that the NT fishery reserve was the most effective to maintain herbivorous fish size, biomass, and richness across all functional groups, though numerical density was not. Total herbivore biomass was 4.3 and 2.8 times higher on NT reefs and GR reefs, respectively than on OA reefs. Among GoA regions, only Ras Mohammed and Sharm El-Sheikh (unfished), and Nabq (fished) met the global mean herbivore biomass target of ~30 kg/500 m2. Our work also highlights three important results regarding the impacts of fishing and fisheries management on herbivorous fish populations: (i) size structure was heavily skewed toward smaller individuals, with fishes less than (20 cm) accounting for 81.1% of the population in heavily fished OA reefs vs. 52.8% at unfished NT reefs, (ii) biomass of larger herbivore individuals (>35 cm) accounting for less than 1% of the total biomass in OA reefs vs. 37% at NT reefs, and (iii) large-bodied target species, Cetoscarus bicolor, Naso unicorn, and Kyphosus spp., accounting for 15.9% of the total biomass at NT reefs on average, while they were virtually absent from OA reefs. Collectively, these findings suggest that many principal fisheries species in the central northern regions of the GoA have been overexploited, which in turn can lead to reef degradation. Therefore, there is an urgent need to develop a participatory management approach and enforce restrictions on destructive fishing gear in order to promote recovery of herbivore biomass.