Fluctuating asymmetry are random deviations of an otherwise symmetrical body plan and arises from instability in development. Earlier studies suggest that levels of cranial fluctuating asymmetry may be influenced by lifestyle and quality of life in a population. It may, therefore, be useful as a stress indicator. We investigated whether cranial fluctuating asymmetry has changed in archaeological Danish populations over time, and between grave sites from the same time period. Our sample consisted of 219 adult individuals from the Neolithic Age (approx. 3000BC) to the Early Modern Age (approx. 1850). We collected 27 3-dimensional landmarks from the face, calvarium, and base of the cranium. Levels of shape variation were analyzed using Procrustes analysis of variance and principal component analysis. Cemeteries, time periods, and sex were compared using linear mixed models, one-way analysis of variance, and Kruskal-Wallis test. We found no statistically significant differences in cranial FA between grave sites from the same time period, nor did we find any statistically significant difference between time periods. We found that sex did not have an influence on levels of cranial FA. We found no measurable difference in levels of cranial FA between Danish populations over time. Further knowledge on genetics and other stress indicators in our sample may give more insight into the relationship between cranial fluctuating asymmetry and developmental instability.