Background: Intimate partner violence (IPV) is a serious global public health issue. Acceptance of wife beating is known to be associated with IPV, but few studies have analysed the acceptance of wife beating from both women and men’s points of view. The objective of this study was to examine whether acceptance of wife beating among couples is associated with lifetime and past one-year physical IPV perpetration towards wives in Nepal. Methods: A cross-sectional study was conducted from August to September 2011, with 717 randomly selected couples with wives aged 18 to 49 years old from the Kirtipur municipality and Bhaktapur district of Nepal. Wives’ and husbands’ acceptance of wife beating was measured by six scale items, while physical IPV experience among wives was measured by seven physical assault scale items. To assess the association between acceptance of wife beating and physical IPV, multiple logistic regression analysis was used. Results: Nearly 30% of wives and husbands indicated that beating of wives is acceptable under certain circumstances. Statistically, no significant difference was detected between wives’ and husbands’ level of acceptance of wife beating. However, husbands’ acceptance of wife beating was positively associated with lifetime and past one-year perpetration of physical IPV, whereas wives’ acceptance of wife beating was neither associated with lifetime nor past one-year victimization of physical IPV. The positive association for husbands remained even after controlling for their partner’s factors. Conclusions: Acceptance of wife beating is an important risk factor, which must be considered to prevent perpetration of physical IPV towards wives in Nepal. Future studies should include men to better understand the structure and dynamics of IPV in Nepal, and prevention programs should also target men to change their attitudes or to identify which couples are at more risk of physical IPV occurring toward wives.