This study aimed to analyze and correlate students’ perceptions of their activities and thinking skills in learning science, as well as compare these perceptions based on school levels. Using descriptive, correlational, and comparative methods, data were collected from 127 students from senior high school and university through a questionnaire containing 52 statements. Descriptive statistics provided an overview of the data, while Pearson’s test analyzed the relationship between students’ perceptions of their activities and thinking skills. An independent sample t-test compared data based on school levels. The results indicated that students perceived their activities as active (mean value of 3.52) and their thinking skills as experienced (mean value of 3.51). A perception of learning activities was correlated with a more perception of thinking skills, although the relationship was not strong (<i>r</i> = 0.357, <i>ρ</i> = 0.000). University students generally had higher perceptions across most activities compared to high school students, suggesting that high school educators might consider adopting some university-level strategies, particularly for motor, emotional, and visual activities, to enhance student engagement and perception. However, there were no significant differences in average perceptions of thinking skills between high school and university students, except for a significant result in likelihood and uncertainty analysis, which highlights a specific area for further investigation. Understanding students’ perceptions of their thinking skills can help educators focus on specific areas for improvement and comprehend how educational transitions impact students’ views on their thinking abilities.