This study investigates the effect of utilizing variation theory approach (VTA) on students' algebraic achievement and their motivation in learning algebra. The study used quasi-experimental non-equivalent control group research design. It involved 114 Form Two students in four intact classes (two classes were from an urban school, another two classes from a rural school). The first group of students from each school learnt algebra in class which used the VTA, while the second group of students in each school learnt algebra through conventional teaching approach. Two-way analysis of covariance and two-way multivariate analysis of variance (MANOVA) were used to analyse the data collected. The result of this study indicated that the use of VTA has significant effect on both urban and rural students' algebraic achievement. There were evidences that VTA has significant effect on rural VTA students' overall motivation in its five subscales: attention, relevance, confidence, satisfaction and interest but it was not so for urban VTA students' motivation. This study provides further empirical evidence that utilization of variation theory as pedagogical guide can promote the teaching and learning of Form Two Algebra topics in urban and rural secondary school classrooms.