The quality of education has been a controversial matter in Afghanistan as many people assume that the quality of education at private schools is better than in public schools and this argumentation is supported by many researchers in the world while in Afghanistan research in this field is very limited. Therefore, this study compared the learning achievement of students in both public and private schools in biology subject of grade 9. Three research questions guide the work. This study conducted in Kabul Afghanistan. The total number of students selected as the sample was 208 (104 male and 104 female) and 22 teachers. These students were selected from 6 public schools and 9 private schools of Kabul province. The paper investigates the educational achievement as revealed test scores. A questionnaire has been used for data collection. The finding from this study shows that the achievement level is low in both types of school. Furthermore, based on the finding from this study, students of public school have a higher mean achievement score compared to students of private schools the achievement gap between schools (public and private ) are 10 points. It is statistically clear that the public school student is outperformed those of private schools student in biology because public school students performed better on a biology test. The advantages of public school student remain even after the family background, teachers’ qualification and schools’ resource were considered. The finding indicated that boys from public schools who have educated parents scored higher than boys student of private schools with the same family background. In addition, girls of public schools have the highest average scores than boys and girls of private schools. When the gender difference was considered the finding shows that, the average scores of girls from both public and private schools are higher compared to boys’ scores of the same level. The achievement gap between boys and girls average scores 6 points.