Attitude has been regarded as a motivating feeling for the learning of biology. However, how inquiry-based learning contributes to attitude change towards the learning of biology has not yet been studied in Rwanda. This study intends to determine the effect of inquiry-based learning on students' attitudes toward learning biology. A sample of 228 secondary school students at the upper secondary level in Rwanda was used. A quasi-experimental design with pre-and post-test was employed. One group was randomly assigned to the control group (N = 109) under the conventional teaching method, while the second group participated as the experimental group (N = 119) under the inquiry-based learning method. Biology attitude questionnaire (BAQ) was tested and a Pearson reliability of 0.89 coefficient was found, and hence the BAQ was adopted and used for the control and treatment groups before and after learning microbiology. Results asserted a significant effect of intervention in favor of the experimental group. However, a significant effect of the treatment on students' attitude change in relation to gender was not identified. The study recommends using inquiry-based learning to promote attitude toward learning biology as it raises students' interest to learning biology and alleviates the difficulty of its concepts.