This longitudinal study explores the effects of an after-school, inquiry-based science intervention on improving low-achieving elementary school children's affective perceptions of learning science (APLS) and positive thinking. Thirty-nine low-achieving children nominated by their teachers attended a three-semester intervention and formed the experimental group; another 87 typical fourth graders were randomly selected as the comparison group. The elementary school student questionnaire was administered to assess all participants' APLS and positive thinking. In addition, eight target students from the experimental group with the lowest scores on either APLS or positive thinking were selected for observation and interviews. Factor analyses, paired-wise t-tests, and theme content analyses were used to compare the similarities and differences between groups and within semesters. It was found that the experimental group children's APLS and positive thinking were gradually and significantly more improved than their counterparts' during the intervention. Interview and observation results were consistent with the quantitative findings. This longitudinal study provided evidence that the after-school, inquiry-based science intervention acted as a facilitating agent for improving low achievers' APLS and positive thinking. Instructional implications and research recommendations are discussed.