Blue - Kivinna til Kivinna (woman to woman - its Swedish) is a really fabulous charity that works for women's right in Africa, the Balkans and the middle east - particularly focused on conflict and post-conflict situations.
They support local women's organisations to play an active role in the peace process.
"Our partner organisations help women legally and psychologically. They are involved in women's health issues and sexual and reproductive rights. They inform women, and men, of women's human rights. They empower and further educate women activists and politicians. They counteract violence against women and human trafficking. They educate authorities and influence decision-making processes and legislation. Women's organisations change society by spreading their knowledge and experience of democracy, reconciliation and peace work."
www.kvinnatillkvinna.se/en/about-us
They are really great, and might be just what you are looking for (...although not solely in Africa).
Alternatively if you find two good charities working in Africa on Education and womens rights and reproductive health respectively, just split your donation and support both (as long as you are making a regular donation, it doesn't matter if its small...)
Although you want to support education, women's rights AND reproductive health, and I understand they do all go together in terms of values etc... it may just be that two different organisations are better at delivering - specialised in delivering different kinds of skills and expertise, working with different government departments etc...they shouldn't necessarily be managed together just because it appeals to donors IYSWIM.