Surprisingly little is known about whether relationships between cognitive and emotional states remain stable or change over time, or how different patterns of stability and/or change in the relationships affect problem solving abilities. Nevertheless, cross-sectional studies show that anxiety/worry may reduce working memory resources, and the ability to minimize the effects anxiety/worry is higher in individuals with greater WM capacity. To investigate the patterns of stability and/or change in cognition-emotion relations over time and their implications for problem solving, 126 14-year-olds’ algebraic WM and worry levels were assessed twice in a single day before completing an algebraic math problem solving test. We used latent transition analysis to identify stability/change in cognition-emotion relations, which yielded a six subgroup solution. Subgroups varied in WM capacity, worry, and stability/change relationships. Among the subgroups, we identified a high WM/low worry subgroup that remained stable over time and a high WM/high worry, and a moderate WM/low worry subgroup that changed to low WM subgroups over time. Patterns of stability/change in subgroup membership predicted algebraic test results. The stable high WM/low worry subgroup performed best and the low WM capacity-high worry unstable across time subgroup performed worst. The findings highlight the importance of assessing variations in cognition-emotion relationships over time (rather than assessing cognition or emotion states alone) to account for differences in problem solving abilities.