Female condoms are the only female-initiated HIV and pregnancy prevention technology currently available. We examined female condom counselling and provision among providers in South Africa and Zimbabwe, high HIV-prevalence countries. A cross-sectional study using a nationally representative survey. All facilities that provide family planning or HIV/sexually transmitted infection (STI) services. National probability sample of 1444 nurses and physicians who provide family planning or HIV/STI services. Female condom practices with different female patients, including adolescents, married women, women using hormonal contraception and by HIV status. Using multivariable logistic analysis, we measured variations in condom counselling by provider characteristics. Most providers reported offering female condoms (88%; 1239/1415), but perceived a need for novel female barrier methods for HIV/STI prevention (85%; 1191/1396). By patient type, providers reported less frequent female condom counselling of adolescents (55%; 775/1411), women using hormonal contraception (65%; 909/1409) and married women (66%; 931/1416), compared to unmarried (74%; 1043/1414) or HIV-positive women (82%; 1161/1415). Multivariable results showed providers in South Africa were less likely to counsel women on female condoms than in Zimbabwe (OR=0.48, 95% CI 0.35 to 0.68, p≤0.001). However, South African providers were more likely to counsel women on male condoms (OR=2.39, 95% CI 1.57 to 3.65, p≤0.001). Nurses counselled patients on female condoms more frequently than physicians (OR=5.41, 95% CI 3.26 to 8.98, p≤0.001). HIV training, family planning training, location (urban vs rural) and facility type (hospital vs clinic) were not associated with greater condom counselling. Female condoms were integrated into provider counselling and care, although providers reported a need for new female-initiated multipurpose prevention technologies, suggesting female condoms do not meet all patient/provider needs or are not adequately well known or accessible. Providers should be included in HIV training efforts to raise awareness of new and existing products, and encouraged to educate all women.