Algebraic thinking in children can bridge the cognitive gap between arithmetic and algebra. This quantitative study aimed to develop and test a cognitive model that examines the cognitive factors influencing algebraic thinking among Year Five pupils. A total of 720 Year Five pupils from randomly selected national schools in Malaysia participated in this study. Two mathematics instruments were used to evaluate the participants’ number, symbol, operation, and pattern senses and their algebraic thinking respectively. Data was analysed using a structural equation modelling and Partial Least Squares regression. The results indicated that the proposed cognitive factors influence algebraic thinking significantly, with the most influential factor being symbol sense followed by pattern sense, number sense, and operation sense. The finding implies that educators should consider implementing activities related to these cognitive factors when teaching mathematics to enhance the pupils’ transition from arithmetic to algebra.