Recent studies demonstrate that brain infiltration of peripheral immune cells and their interaction with brain-resident cells contribute to Parkinson’s disease (PD) pathology. To investigate an interaction of T cells and brain-resident cells in the midbrain in spatial manner, we developed a three-dimensional (3D) human model comprising stem cell-derived human midbrain organoids (hMO) and peripheral blood T cells. We demonstrated that the complex 3D structure of organoids consists of multiple midbrain-specific cell types, allowing to study T cell motility and T cell interactions with midbrain tissue in a spatially organized microenvironment. We tested different co-culture conditions and determined optimal settings for studying T cell driven effects on hMO. T cells infiltrate hMO tissue and cause neural cell loss in hMO. Our work establishes a novel 3D cell co-culture model as a promising tool to investigate the effect of the adaptive immune system on midbrain in the context of PD.