Government reforms such as the general education quality improvement program for equity are implemented to address concerns about educational inequality. However, studies advancing understanding of the patterns of gender inequality in achievement in conflict affected areas are rare. The purpose of this article is to examine patterns in gender inequality in General Secondary Education Certificate Examination results in Math, English, and Aptitude for 2021, 2022 and 2023 academic years in conflict affected areas. The data consist of achievement scores from 45 schools and a total of 32,528 students, obtained from the Education office of North Wollo Zone, Northeast Ethiopia. Using multilevel modeling, within- and between-school inequalities, achievement inequalities in gender, effects of teacher qualifications on achievement, and variations in gender-achievement relationships are examined. Student performance has been found to have consistently declined in the last two years in math, English and aptitude scores. On average, boys perform significantly higher than girls on these subjects consistently during the normal and conflict seasons. Inequality has decreased in conjunction with declining student performance, and inequalities due to school characteristics are much lower than inequalities due to student differences. School inequality declines in years of conflict compared to normal ones. The relationships between gender and achievement also vary statistically from school to school, with the conflict exacerbating existing inequalities. Based on the results, it is suggested that equity strategies should consider inequalities with declining student performance as opposed to conventional inequalities with high and low performing groups. Future research may isolate the effects of conflict and reforms in national testing procedures to account for gender inequalities.