The first schools were created by the French at the beginning of the colonial period and were not widely accepted by the people of Mali. Families did not want their sons, let alone their daughters, to attend these institutions, so the education of girls was stunted from the start. After Mali gained its independence in 1960, efforts were made to reform the education system by improving the quality of education and making it equally accessible to men and women. Despite these reforms, girls are still enrolled at a far lower rate than boys, even in primary school. According to GenderNet, in 1999 only 44% of girls were enrolled in primary school as compared to 63% of boys. Secondary school enrollment falls to 10% and 19% respectively. 

As it stands today, the public education system in Mali is set up in three stages: elementary school (6 years), junior high school (3 years), and high school (3 years). To receive an engineering degree students must complete another two years at a college or university, and then three to four more years at a engineering institution. As in many African countries, students must pass certain exams in order to move on to the next education level. Students must earn a CFEPCEF (Certificat de Fin d'Etude du Premier Cycle de l'Enseignement Fondamental) degree upon completion of elementary school and a DEF (Diplome d'Etude Fondamental) degree after junior high school. Upon finishing high school, students earn a BAC (Baccalaureat Malien), and after college students earn a CAP certificate (Certificat d'Aptitude Professionnelle). After finishing engineering school (Grande Ecole d'Ingenierie), students earn a Licence or Maitrise (Bachelors or Masters degree). Admittance to the grand ecoles is very competitive and based on entrance exam scores.

Malian educational institutions are generally poorly equipped due to a lack of textbooks and audio/visual equipment, so most courses are in lecture format. Laboratories lack equipment for experiments, and computers are not found in primary and secondary schools. Computers are mainly found at the college/university level and in the engineering and business Grande Ecoles.' 

There are a few institutions that accept only female students. Notre Dame du Niger high school accepts an average of 316 students every year for general study courses, and another 180 students for science study. Cours Jean d'Arc is a private institution that accepts an average of 230 students each year for secretary and business/technician studies. However, many women are educated in an informal manner through women's associations, non-governmental associations, and the Education Center for Development. 

For women who do take part in the public school system, at the end of junior high school an education committee is in charge of advising the student on her future based on school performance and the candidate's suggestions. These advisors may not always give the best advice and the student's family may also try to influence their choices, which can lead to an unsuccessful outcome later.

Women in Mali generally do not have the opportunity to pursue technical education due to low participation in the education system and an overall lack of encouragement. There are very few women in high positions to serve as role models and it is generally expected that women will raise families as opposed to pursuing a career. However, thanks to the efforts of the government and various organizations the percentage of girls enrolled in school has been steadily increasing over the past decade. In addition, younger women are less likely to feel that they are confined only to family duties, and they are more aware of the opportunities available to pursue professional careers. 

Organizations such as AFIMA (Women Engineers Association of Mali) and FEMSA (Girls Education in Math and Science in Africa) actively campaign for increased awareness of science careers for women. Others deal with the promotion of science and greater educational access for women in general. Those organizations are: the Malian Ministry of Education, Girls Schooling Organism, AMASEF-FAWE (the Malian Association for Schooling and Education of Girls / Female Educators Forum in Africa); SAGE; CAFO (Coordination of associations and non governmental organizations of Mali); and SMM (Mathematics Society of Mali).