Learning outcomes is one of the most important aspect of learning variables. Learning outcomes are influenced by condition of learning and learning methods. Problem solving method and brainstorming method can be used to improve learning outcomes. Object of this research is 50 students of PGSD FKIP UNDANA, which is divided into 2 groups with 25 students in each class. The first class used problem solving method, and the other used brainstorming method. Both methods are connected to learning motivation to asses learning outcomes of science subject. This research uses factorial design which is factorial 2x2 with random assignment to treatment. Research instrument was used to measure learning outcomes which are pre and posttest, questionare was used to measure motivation and learning outcomes of analysis and understanding science concepts with hypothesis that used 2 ways anova. The results show that; there is a difference in learning outcomes between problem solving method and brainstorming method with F 27.071 with (sig).000p. 0.05. There is also difference in learning outcomes of student with high and low motivation with F 75.389 with (sig).000p. 0.0.05. This research also found that learning outcomes are affected by learning method and learning motivation (.039 0.05)