Reform efforts for science education urge inquiry as a central strategy of science instruction. This study investigated high school students’ perceptions about an inquiry-based class and examined to which level the students took lead in generating questions, collecting data, and interpreting results in science inquiry. Factors that may have influenced the students’ attitude toward inquiry-based instruction and learning outcomes were also examined. 34 11th grade high school students in a microbial fuel cells (MFCs) course participated in this study. Data was collected through Student Conceptions on Inquiry Science Learning (SCISL), Student Science Learning Achievement (SSLA), and Attitude toward Inquiry-based Learning (AIL) questionnaires. The results indicated that after taking the course, students’ learning outcomes including affective and cognitive performance in MFCs course improved significantly. The study results also revealed that the high school students and the teacher perceived the class environment differently on whether the science class is constructed as being student-initiated or teacher-guided inquiry. In addition, factors such as students’ demographic characteristics, confidence in inquiry learning, prior knowledge, and personality traits were explored. The study results can provide important implications in the understanding of students’ learning behaviours for inquiry learning.