Bioinformatics is a growing research field that received great notoriety in the years of the COVID-19 pandemic. It is a very integrative area, comprising professionals from science, technology, engineering, and mathematics (STEM). In agreement with the other STEM areas, several women have greatly contributed to bioinformatics ascension; however, they had to surpass prejudice and stereotypes to achieve recognition and leadership positions, a path that studies have demonstrated to be more comfortable to their male colleagues. In this review, we discuss the several difficulties that women in STEM, including bioinformatics, surpass during their careers. First, we present a historical context on bioinformatics and the main applications for this area. Then, we discuss gender disparity in STEM and present the challenges that still contribute to women’s inequality in STEM compared to their male colleagues. We also present the opportunities and the transformation that we can start, acting in academia, inside the family and school environments, and as a society, hence contributing to gender equality in STEM. Finally, we discuss specific challenges in the bioinformatics field and how we can act to overcome them, especially in low and middle-income countries, such as Brazil.