The T-bar penetrometer is extensively used in offshore field investigation and laboratory testing to evaluate the undrained shear strength of soft clay because of its reliability and repeatability in measurements. However, most previous studies on T-bar penetration have adopted a deterministic approach and focused solely on homogeneous soils, neglecting the geological uncertainty caused by the spatial variability of soil. To remedy this situation, this study aimed to investigate the effect of soil spatial variation on the T-bar penetration process in soft clay by employing large deformation random finite element modeling. The findings indicate that the variability in soil strength substantially modifies the flow pattern and failure mechanism of the soil, consequently influencing the penetration resistance factor of the T-bar. It was observed that the resistance factors follow the log-normal distribution. A relationship between the probability of failure as well as the factor of safety was determined, allowing for a clear assessment of the reliability level associated with varying factors of safety. To allow for this effect, a practical framework is developed to correct T-bar penetration data to estimate soil strength.