Thermal barrier coatings (TBCs) applied to in-cylinder surfaces of a low temperature combustion (LTC) engine provide an opportunity for enhanced efficiency via two mechanisms: (i) positive impact on thermodynamic cycle efficiency due to combustion/expansion heat loss reduction, and (ii) enhanced combustion efficiency. Heat released during combustion increases the temperature gradient within the TBC layer, elevating surface temperature over combustion-relevant crank angles. Thorough characterization of this dynamic temperature “swing” at the TBC–gas interface is required to ensure accurate determination of heat transfer and the associated impact(s) on engine performance, emissions, and efficiencies. This paper employs an inverse heat conduction solver based on the sequential function specification method (SFSM) to estimate TBC surface temperature and heat flux profiles using sub-TBC temperature measurements. The authors first assess the robustness of the solution methodology ex situ, utilizing an inert, quiescent environment and a known heat flux boundary condition. The inverse solver is extended in situ to evaluate surface thermal phenomena within a TBC-treated single-cylinder, gasoline-fueled, homogeneous charge compression ignition (HCCI) engine. The resultant analysis provides crank angle resolved TBC surface temperature and heat flux profiles over a host of operational conditions. Insight derived from this work may be correlated with TBC thermophysical properties to determine the impact(s) of material selection on engine performance, emissions, heat transfer, and efficiencies. These efforts will guide next-generation TBC design.