Increasing number of refrigeration units has led to an increase of CO2 emissions and the destruction of the ozone layer. Using low global warming potential (GWP) refrigerants, improving the efficiency of vapour compression refrigeration (VCR) units, and minimising refrigerant leakages can reduce the global warming effect. Investigating the refrigerant distribution under varied operating conditions can provide a deeper understanding of refrigerant charge optimization. This study proposed a model of refrigerant mass distribution in a prototype oil-free VCR system using a linear compressor with variable strokes and R134a. The absence of the oil lubricant allows the adoption of compact heat exchangers, such as micro-channels, so that the total refrigerant charge can be reduced significantly. The predicted total refrigerant charge has a Mean Absolute Percentage Error (MAPE) of 3.7%. The simulation results indicate that refrigerant distributed in the condenser is most sensitive to operating conditions and total refrigerant charges. The refrigerant accumulated in the condenser is 6.8% higher at a total refrigerant charge of 0.33 kg than that of 0.22 kg. For a total refrigerant charge of 0.33 kg, 72.1% of the total refrigerant can accumulate in the condenser. At a fixed pressure ratio, the refrigerant as a two-phase form in the condenser decreases slightly with the increase of compressor strokes, resulting in a larger mass flow rate, thus cooling capacity. The present model can be adapted for optimization of a refrigeration unit and its components.