We compared population structure and trophy hunting statistics of Himalayan ibex (Capra sibirica) in two community-controlled hunting areas (CCHAs) of northern Pakistan with varying duration of trophy hunting and isolated populations of C. sibirica. Based on fixed-point direct count method during winter 2016–2017, 939 ibexes were counted in Khyber and 346 in Hussaini, with a density of 7.5 and 3.2 animals km^-2, respectively. Though the populations of C. sibirica at both the study sites have increased compared to the past estimates, we found variations in population structures and horn sizes, presumably as a result of trophy hunting. The sex ratios are skewed toward females in Khyber (87 males/100 females) and towards males in Hussaini (115 males/100 females). The trophy size males were 7% of the population in Khyber and 11% in Hussaini. Mean group (herd) size in Khyber was 28 (range = 1–117) and Hussaini was 20 (range = 1–79). Mean horn size of the trophies harvested in Khyber was 102 cm (± range = 91–114) compared to 108 cm (range = 99–121) in Hussaini. Stringent regulatory measures are suggested to determine the number of permits.