This paper investigates the effects of different inlet flow profiles on thermal mixing within a T-junction using CFD simulations with the IDDES-SST turbulence model. The different combinations of inlet flow profiles are related to different stage in the flow entry region. The effects of the inlet flow profile on the mean and transient flow behaviour are assessed, while a spectral proper orthogonal decomposition and power spectral density analysis are performed to assess the underlying flow structures and the predominant frequency modes. It is found that the vortical structures associated with the horseshoe and hovering vortex systems consist of a single roll-up vortex for cases with uniformly distributed boundary conditions (BCs) at the branch inlet whereas a double roll-up vortex is observed for the other cases. The double roll-up vortex enhances the mixing locally due to the entrainment of fluid from the branch pipe in these vortical structures, which then results in a lower mean temperature distribution. The appearance of the secondary vortex pair and the nested vortices is delayed for cases with uniformly distributed BCs at the branch inlet, which again results in lower thermal mixing and consequently higher values of mean temperature when compared with the other cases. It is also found that the vorticity related to the counter-rotating vortex pair as well as to the second pair of vortices rotating in the opposite direction is higher for cases with uniformly distributed BCs at the branch inlet. Lastly, the combinations of inlet flow profiles lead to different coherent structures, and the dominant frequencies are of a Strouhal number of around 0.7 for uniformly distributed profiles at the branch inlet and in the range 0.4–0.5 for the other cases.