In the framework of the functional renormalization group and of the perturbative, algebraic approach to quantum field theory (pAQFT), in D’Angelo et al. [Ann. Henri Poinc.25 (2024) 2295–2352] it has been derived a Lorentzian version of a flow equation à la Wetterich, which can be used to study nonlinear, quantum scalar field theories on a globally hyperbolic spacetime. In this work, we show that the realm of validity of this result can be extended to study interacting scalar field theories on globally hyperbolic manifolds with a timelike boundary. By considering the specific examples of half-Minkowski spacetime and of the Poincaré patch of Anti-de Sitter, we show that the form of the Lorentzian Wetterich equation is strongly dependent on the boundary conditions assigned to the underlying field theory. In addition, using a numerical approach, we are able to provide strong evidences that there is a qualitative and not only a quantitative difference in the associated flow and we highlight this feature by considering Dirichlet and Neumann boundary conditions on half-Minkowski spacetime.