Considering the urgent need to mitigate carbon emissions in the building sector, this study aimed to reduce carbon emissions during the operation of thermally active building systems (TABS) in Japan. TABS and all-air systems (Variable Air Volume systems, VAV system) were compared through a dynamic energy simulation for a small office model using Energy Plus in two target regions namely, Tokyo and Kyushu, Japan. The annual primary energy consumption of the Heating, Ventilation, and Air Conditioning (HVAC) systems were calculated. The obtained annual primary energy use was converted to operational carbon emissions by multiplying it with carbon intensity. Results indicated that annual primary energy consumption by TABS was lower than those from the VAV systems. Furthermore, the dynamic carbon intensity, which accounts for the timing of power consumption and is more appropriate for the region where the power is consumed, was calculated. This dynamic carbon intensity was determined based on the actual performance of thermal power generation. By applying dynamic car-bon intensity, operational carbon emissions were lower in regions where dynamic carbon intensity remained low for both TABS and VAV systems. Additionally, TABS control strategies were evaluated based on operational carbon emissions using dynamic carbon intensity. Among the different water supply schedules (21,00–9:00, 0:00–12:00, 3:00–15:00, and 6:00–18:00), operational carbon emissions were slightly lower when the supply began earlier. Operational carbon emission reductions from daytime operation, with lower dynamic carbon intensity, and nighttime operation, which reduces heat source capacity and distributes the heat load, were approximately equal.