In recent years, the sustained increase in the worldwide demand for lithium batteries goes side by side with the need for reliable methods to assess battery performance. Of particular importance is assessing Lithium-Ion cell’s thermal behavior given its role on hazard and aging of batteries. An essential task towards developing battery management systems is the estimation of physical parameters and their uncertainties in terms of both models and observations. Consequently, this paper analyzes the uncertainty in a thermal single particle model for a lithium-ion cell. In the first part of the manuscript, we explore the model adequacy by analyzing the forward and backward uncertainty propagation in the model in terms of diffusion coefficients, reaction rate constants, and observations of cell voltage. In the second part of the manuscript, we infer the cell’s reversible heat given the energy balance equation and the cell’s temperature observations. We argue that the methods proposed here may be extended to analyze other more general lithium-ion models.