This paper investigates the effects of different inlet velocity profiles on thermal mixing and conjugate heat transfer (CHT) within a T-junction. The flow domain is modelled using the Improved Delayed Detached Eddy Simulation (IDDES) turbulence model implemented within the commercial CFD software STAR-CCM+ 2020.1.1. The thermal analysis of the solid domain is also addressed within the CFD simulations. The OECD/NEA-Vattenfall experimental benchmark database is used to validate the CFD model. The effect of mesh sensitivity within the CFD simulations is also studied qualitatively and quantitatively. The influence of different inlet flow profiles on the CFD simulations is then assessed. Different combinations of inlet flow profiles, uniformly distributed and fully developed, are considered. Compared to the flow profile at the main pipe inlet, the flow profile at the branch pipe inlet presents a much more significant effect on the mean temperature distribution downstream of the T-junction. It is found that the flat flow profile at the branch inlet causes a higher temperature at the top wall, therefore a larger temperature gradient, and may lead to higher thermal stresses due to thermal stratification. The temperature distribution is more uniform for cases with the fully developed flow profile at the branch inlet. The variance of temperature is high at the sides of the pipe, regardless of the velocity profile used. The combination of flat flow profiles at both inlets causes the highest temperature variance. Moreover, the regions of maximum variance of temperature are located at different positions along the pipe section, depending on the combinations of inlet flow profiles.