Measurement of the physical properties of high-temperature molten salts is important for the efficient design and operation of molten salt reactors (MSR) in which the reactor coolant and nuclear fuel are in a homogeneous liquid state. Although some crucial physical properties such as viscosity, thermal conductivity, density, etc., have been drawing much attention, relative data, especially for molten chloride salts, are scarce. Thus, it is urgent to prepare the viscosity data as one of the key transport properties in thermal hydraulics analysis. However, it is not an easy task to measure the molten salt viscosity with high accuracy due to end effect, a small gap between the chamber and spindle, thermal expansion of the chamber and spindle at high temperatures in a rotational viscometer. Additionally, molten salt temperatures inside furnace are not uniform due to the large temperature gradient inside the chamber, and therefore the assumption of laminar condition can be violated. In this study, geometric factors, which can be a major interference in the torque measurement, were considered for the accurate determination of the viscosity. We established a high-temperature molten salt viscosity measurement system with Brookfield rotational viscometer. KNO3 molten salt was used as a model substance at a temperature range of 650–773 K. In-house designed spindles and chambers were made of corrosion-resistant alumina. Thermal expansion has a significant influence on the size and shape of the chamber and spindle. The effect of thermal expansion on the conventional correction method was examined with temperature variation and distribution. Gap size variation was also investigated in order to improve the accuracy.