Many households in Mongolia are facing increased livelihood and financial insecurity due to rapid social, economic, political, and climate changes. There is concern regarding the effects of a loss in livelihoods and shifting gender roles on family dynamics in these households. This historical cross-sectional study explores patterns of father presence and father engagement with children under five in Mongolia between 2000–2013 using Multiple Indicator Cluster Survey (MICS) data. Trend analyses were performed to explore changes in father presence and engagement from the four most recent datasets. Patterns were explored for demographic subgroups such as region of residence, urban/rural residence, child’s sex, and whether the household owned livestock. Multivariate logistic regression was also performed to adjust for potential confounding variables and covariates. The national point-prevalence of father presence fluctuated from 78–83% while father engagement fluctuated between 40–49% across the survey time-points. These fluctuations were only significant for father presence. Significant changes in father presence and engagement were evident in the Khangai, Central, and Ulaanbaatar regions, while in the Western region only significant changes for father engagement were found. Logistic regression showed a change in point-prevalence of father engagement between 2005 and 2010 and between 2005 and 2013, and changes in father presence and engagement over time remained significant after controlling for other covariates such as SES. The changes in father presence and engagement in many households may be due to the economic insecurities brought about by rapid macro-environmental changes.