Background Cross-cultural studies studying work-family conflicts (W_F_Cs) are scarce. We compared the prevalence of W_F_Cs, factors predicting it, and its association with self-rated health between Japan and Egypt. Methods Among 4862 Japanese and 3111 Egyptian civil workers who were recruited by a convenience sample in 2018/2019 and reported self-rated health status, we assessed the W_F_Cs by the Midlife Development in the US (MIDUS) and attributed it, by linear regression analyses, to sociodemographic, family, and work variables, and assessed its gender- and country-specific associations with self-rated health by logistic regression analyses. Results W_F_Cs were more prevalent in Egyptian than Japanese women (23.7% vs. 18.2%) and men (19.1% vs. 10.5%), while poor self-rated health was more prevalent in Japanese than Egyptians (19.3% and 17.3% vs. 16.9% and 5.5%). In both genders of countries, longer working hours, shift work, and overtime work predicted higher scores of the work-to-family conflict (WFC). In contrast, single status predicted lower scores of the family-to-work conflict (FWC). Living with children, fathers, or alone in Japan, while education in Egypt was associated with the conflicts. The OR (95% CI) for poor self-reported health among those with the strong, in reference to weak W_F_Cs, was 4.28 (2.91-6.30) and 6.01 (4.50-8.01) in Japanese women and men and was 2.46 (1.75-3.47) and 3.11 (1.67-5.80) in Egyptian women and men. Conclusions Japanese and Egyptian civil workers have different prevalence and correlated factors of W_F_Cs and self-rated health. W_F_Cs were associated in a dose-response pattern with poor-self-rated health civil workers of both countries.