The main purpose of this study was to assess the contribution of women academic leaders and their challenges in higher education in Ethiopia, in the case of three generation universities. The study focused on the Amhara region higher education institutions in Bahir Dar, Debre Markos and Debre Tabor Universities. The three generation universities were selected by using a purposive sampling method. The total participant of the study were 122 both 110 for questionnaires and 12 for interviewing. The researcher used simple random sampling for male academic leaders, comprehensive sampling techniques for women academic leaders and purposive sampling techniques for top level academic leaders. To achieve the purpose of the study, the researcher employed pragmatism paradigm, mixed method approach and convergent parallel design. Questionnaires and in-depth interview were employed for data collection instrument. SPSS version 20 was used for quantantive data. Frequency distribution, percentage, means and standard deviation were employed. From the Inferential statistics the researcher was using one way ANOVA, independent sample t-test and one sample t-test was employed in analyzing data. Because of it provide better result about the study .The finding of the study was employed about the contribution of women academic leaders and their challenges at a higher education institution in three generation universities similar results based on ANOVA result.Regarding the contributions of women academic leaders, they are highly play in facilitating teaching learning process, executing the rule and regulation of the university, and participating community service practice in their position. On the other hand, regarding the challenge of women academic leader’s social and organizational problems are the major factors that affect the contribution of women academic leaders at higher education institutions in Ethiopia. Lastly, based on the findings and conclusions, recommendations were forwarded to alleviate some of the existing challenges affecting the contribution of women in leadership positions in higher education institutions.