Some children struggle with mathematics. Among these children, some of them may be learners with mathematical difficulties. While research has revealed multiple deficits as candidate causes for mathematical difficulties and probable subtypes, the cognitive profiles of these subtypes are not fully understood. Moreover, we have yet to discover whether children may move in or out of these subtypes over time. This study set out to identify the subtypes of mathematical difficulties as well as their stability. Using cluster analyses, we discovered 5 distinctive subtypes among children with mathematical difficulties over the first 2 years of elementary school: the number sense deficit subtype, the numerosity coding deficit subtype, the symbolic deficit subtype, the working memory subtype, and a mild difficulty group. These subtypes showed moderate stability. While some subtypes appeared to be somewhat stable over time, some developed into another profile of deficits and still some emerged only at later points in the development. Understanding the cognitive profiles of different subtypes of mathematical difficulties can better help researchers and educators to devise intervention strategies that build on what the children are able to do and improve what they are still struggling.