The study investigated the impact of virtual laboratory on the achievements of secondary school chemistry students in homogeneous and heterogeneous collaborative settings in Minna, Niger state, Nigeria. Three hypotheses were formulated, analyzed and tested at 0.05 alpha level. Stratified sampling technique was used to select 60 Senior Secondary Class Two (SS II) Chemistry Students. The subjects were stratified along gender and ability levels. Sixty students were randomly selected from two secondary schools in Minna, Nigeria. Thirty students (male, n = 15; female, n = 15) were selected from each school. Pretest, posttest, and experimental group design was employed. Experts validated 20-item multiple-choice Chemistry Achievement Test (CAT) was used for data collection. A reliability coefficient of 0.91 was obtained from the pilot testing using Kuder Richardson (KR-20). ANCOVA and Sidak post-hoc statistics were used for testing the hypotheses at 0.05 level of significance. The results showed that: (a) students in homogeneous ability grouping taught Chemistry using virtual laboratory instruction in collaborative setting performed better than their counterpart taught Chemistry in heterogeneous grouping composition; (b) female students in homogeneous group performed better than their counterparts in heterogeneous groups; (c) the higher achiever students in homogeneous groups outperformed those in heterogeneous groups. Based on these findings, it was recommended that the use of virtual laboratory instruction in homogeneous gender and ability level grouping in collaborative setting should be encouraged in teaching practical chemistry at senior secondary schools in Nigeria.