This study established the effects of a web-based computer simulation on the conceptual understanding of the rate of chemical reaction and attitude of 66 first year secondary school (SS1) students in Niger state, Nigeria towards chemistry. A pretest and post-test experimental design was used during which students were randomly assigned into either the experimental or the control group. The 'Rate of Reaction Knowledge Test' (RRKT) and the 'Chemistry Attitude Scale' (CAS) was administered. Classroom observations and structured interviews with the students yielded additional qualitative data. The results showed that a statistically significant difference was found between the groups and that the web-based computer simulation improved students' development of mental models on rate of reaction in comparison to the students in the experimental group. The students in the experimental groups also indicated that they liked using the software learning tools. The findings support the notion that chemistry teachers should be trained or re-trained in the use of web-based computer simulations for teaching chemistry. It places an onus on educational authorities to procure web-based simulations for use in teaching chemistry and other science subjects in secondary schools.