Absolute stellar ages and masses are some of the most sought after astrophysical quantities, particularly for young stellar systems, but accurate determination of these quantities has remained elusive due to a necessary reliance on theoretical stellar structure and evolution models. This review focuses on the theoretical development of early stellar evolution models, including modern additions of non-standard physics, and provides suggestions about where theory and observations can advance our present understanding about young star physics to improve model mass and age predictions. The approach to modeling young stars has remained largely unchanged since the advent computers in the mid-twentieth century: pre-main-sequence stars are assumed to be "born" with an initially large radius before undergoing quasi-hydrostatic contraction, governed by the standard stellar structure equations, until they reach the main sequence. Comparing predictions from canonical models of early stellar evolution against observational data of young eclipsing binary systems and young stellar populations shows that canonical models reproduce a number of key observational features. While broadly describing observed features of young stars and stellar populations, observations also reveal that the canonical approach provides an incomplete description of early stellar evolution. It is now clear that canonical models underestimate masses of pre-main-sequence objects by 50%, yield effective temperature dependent ages for young stellar populations, and fail to predict a unique age even for individual objects. These issues are now commonly believed to be the result of uncertainties in existing model physics, and physics entirely missing from early stellar evolution models. Recent efforts incorporating non-standard physics – accretion, magnetic fields, rotation – are starting to reconcile some of the observed disparities. However, there are fundamental uncertainties and limitations when modeling these physics that currently preclude a coherent understanding about their role in early stellar evolution.