In buildings, HVAC systems consume a high amount of energy to provide thermal comfort for occupants. A methodology is presented in this paper to control thermostat operation of the buildings considering the effects of indoor and outdoor boundary conditions and phase change material (PCM) characteristics. EnergyPlus v8.1 building energy simulation software was used to analyze the energy performance of the PCM incorporated building models and to implement Fanger model to control HVAC thermostat operation according to BS EN 15251:2007 thermal comfort categories. Three types of building HVAC schedule, PCM with different melting points and layer thicknesses were studied for Madrid climate zone. Moreover, the impact of occupants clothing on the energy consumption was investigated. Furthermore, payback analysis was conducted to find out the economic benefits of PCM integration into the building envelopes. Application of PCM improved the cooling and heating energy performances except for the office model in winter (heating period). Additionally, higher energy savings and lower payback periods were observed when PCM with higher melting point was applied to the buildings. Eventually, energy savings in PCM incorporated models were found to improve further when occupants changed their clothing behavior in winter.The work is partially funded by the Spanish government (ENE2011-22722). The authors would like to thank the Catalan Government for the quality accreditation given to their researchgroup (2014 SGR 123). The research leading to these results hasreceived funding from the European Union’s Seventh FrameworkProgram (FP7/2007-2013) under grant agreement no. PIRSES-GA-2013-610692 (INNOSTORAGE). Alvaro de Gracia would like tothank Education Ministry of Chile for Grant PMI ANT 1201. Svetlana Ushak acknowledges to CONICYT/FONDAP no. 15110019 SERC-Chile, and PMI ANT 1201 for the financial support