Heating, ventilation, and air-conditioning (HVAC) systems account for almost half of the energy consumption in buildings. By benefiting from advancements in information and communication technology, human-in-the-loop HVAC operations have drawn considerable attention in the last decade with the aim of curtailing unnecessary energy use and providing user-specific comfort zones with reduced user dedication. Future progress in thie field calls for an in-depth understanding of the current state and challenges of the human-in-the-loop HVAC systems. Therefore, using a structured literature review approach, we have investigated this field according to two parameters of human dynamics that drive user-centric operations of HVAC systems, namely, occupancy and comfort. In this review and assessment study, by proposing a five-tier hierarchical taxonomy, we have classified the studies based on their contributions to occupancy- and comfort-driven human-in-the-loop HVAC operations (e.g., occupancy detection or comfort profiling) and have presented categorization for techniques and their quantitative performance assessment In doing so, we have accounted for the context of the studies as they relate to developments in residential and office buildings given that distinct circumstances in each context (e.g., accessibility to thermostats) have resulted in different methodologies, especially in adopting the sensing techniques and HVAC operations. Moreover, we have distinguished simulations from field evaluations to assess the actual viability and challenges in achieving desirable results in practice. Lastly, the Hype cycle model was utilized to qualitatively evaluate the developments of different technologies for human-in-the-loop HVAC operations from a research perspective.