Biology learning in MA (Madrasah Aliyah) Khas Kempek was still dominated by teacher with low students involvement. This study would analyze the effectiveness of the 5E (Engagement, Exploration, Explanation, Elaboration, Evaluation) learning model in improving scientific knowledge and problems solving. It also explained the relationship between students scientific reasoning with their problem-solving abilities. This was a pre-experimental research with one group pre-test post-test. Sixty students of MA Khas Kempek from XI MIA 3 and XI MIA 4 involved in this study. The learning outcome of the students was collected by the test of reasoning and problem-solving. The results showed that the rises of students scientific reasoning ability were 69.77% for XI MIA 3 and 66.27% for XI MIA 4, in the medium category. The problem-solving skills were 63.40% for XI MIA 3, 61.67% for XI MIA 4, and classified in the moderate category. The simple regression test found a linear correlation between students scientific reasoning and problem-solving ability. This study affirms that reasoning ability is needed in problem-solving. It is found that application of 5E learning model was effective to improve scientific reasoning and problem-solving ability of students.