In this work, we present an upscaled model for mixed dimensional coupled flow problem in fractured porous media. We consider both embedded and discrete fracture models (EFM and DFM) as fine scale models which contain coupled system of equations. For fine grid discretization, we use a conservative finite-volume approximation. We construct an upscaled model using the non-local multicontinuum (NLMC) method for the coupled system. The proposed upscaled model is based on a set of simplified multiscale basis functions for the auxiliary space and a constraint energy minimization principle for the construction of multiscale basis functions. Using the constructed NLMC-multiscale basis functions, we obtain an accurate coarse grid upscaled model. We present numerical results for both fine-grid models and upscaled coarse-grid models using our NLMC method. We consider model problems with (1) discrete fracture fine grid model with low and high permeable fractures;(2) embedded fine grid model for two types of geometries with differnet fracture networks and (3) embedded fracture fine grid model with heterogeneous permeability. The simulations using the upscaled model provide very accurate solutions with significant reduction in the dimension of the problem.