It is becoming often to measure steady-state heat transfer rate from thermal systems with variable speed and volume equipment and hence with fluctuating properties and mass flow rates. However, it is unclear if the conventional heat transfer rate measurement based on averages of temperature and pressure measurement is representative enough to represent the effect of system dynamics and measure their heat transfer rates accurately. This paper studied the issue by comparing its accuracy and uncertainty to that of alternative data-processing methods with theoretically less systematic bias. The comparison was conducted with steady-state data from a variable-speed ductless heat pump (DHP) system with occasional fluctuation of refrigerant flow and properties. The results show that the accuracy improvement brought by one alternative method is statistically significant albeit small in magnitude, and the other method may reduce uncertainty of the heat transfer rate measurement in tests with large periodic changes of measured variables. Nonetheless, both alternative methods are about 100 times more computationally expensive than the conventional averaging method, and averages of temperature and pressure measurement are still appropriate when computational resources are limited.