Since 2018 she has been a full professor at Utrecht University, holding the chair Longitudinal Data Analysis at the Department of Methodology and Statistics.

Hamaker returned to the Netherlands in 2006, being appointed assistant professor at the Department of Methodology and Statistics, Utrecht University.

She is also an advocate of within-person thinking in social sciences,[7] pointing out that conclusions based on cross-sectional data do not necessarily generalize to the processes within a particular person.

Since 2015 Hamaker has collaborated frequently with Bengt O. Muthén and Tihomir Asparouhov in the development of the Dynamic Structural Equation Modeling, a module that allows for Bayesian time series analysis in the software package Mplus.

[9] Throughout her academic career, Hamaker has served as associate editor of Multivariate Behavioral Research.