In this paper, we investigate the teaching of science subjects before and after the lockdown and explore the factors that affect students’ confidence in passing national examinations. The research was carried out in the districts of the Kigezi region in Uganda, where 435 students from 12 schools and 60 science teachers provided both qualitative and quantitative data on the state of science education before, during and post the Covid-19-induced lockdown through interviews and questionnaires. Multiple regression analysis was performed to establish the relationship between syllabus coverage, practical coverage, likability of the science subjects, and confidence in passing both school and national examinations. We note that poor syllabus coverage and lack of adequate practical time are often blamed for the poor pass rates in science subjects in secondary schools in Uganda, but this research indicates that blaming these two alone is simplistic at best. Our results show that although the two factors are important to students by themselves, they are not the only determinants of students’ confidence in success in national examinations. We show that subject likability is an indispensable determinant of students’ confidence in passing science subjects in national examinations, and together with practical teaching as well as syllabus coverage, a winning formula for improving confidence in passing and ultimately enrollment is obtained. From this, we conclude that improving students’ attitude and perception of science should be emphasized as much as advocacy for practical teaching and completion of the syllabus in time. This will improve students’ perception and performance in the sciences with the overall effect of boosting retention rates in STEM subjects.