Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, threatens oilseed rape (Brassica napus) crops internationally. The development of this disease is strongly controlled by the weather, which is why global climate change is likely to influence its spread and impact. Climate change may affect the pathogen directly or indirectly via the host plant. This study investigates the potential impact of climate warming on Sclerotinia stem rot severity in oilseed rape in Poland. The aim of this investigation was to assess the relationship between the direct impact (DI) and indirect impact (II) of climate change on disease severity using the 4.5 and 8.5 representative concentration pathways (RCPs). Under the RCP4.5 scenario, nearly 60% of the simulations performed for 16 regions in four periods (2020–2039, 2040–2059, 2060–2079, 2080–2099) showed reductions in disease severity in comparison to those conducted for 1986–2005, while under RCP 8.5, this reduction was generated for nearly 90% of the cases. The effect of the RCP scenario on clustering the regions according to the value of Sclerotinia stem rot severity was also investigated. The simulations revealed that, for all periods, the lowest disease severities are expected for Zachodniopomorskie and Pomorskie. The results obtained also show the superior effects of the II over the DI on Sclerotinia stem rot severity in the future. Under the RCP4.5 scenario, the rate of IIs was greater than that of DIs for 10 regions, while under RCP8.5, this relationship was registered for 16 regions. These outcomes result from the acceleration of the oilseed rape flowering period triggered by expected temperature increases. The novelty of this study lies in a detailed analysis of the relationships between the DI and II of climate change, expressed numerically, for 16 regions in Poland. The obtained results highlight the role of the indirect impact in shaping disease severity and indicate that it should be incorporated into assessment methods of climate change effects alongside the direct impact.