This study presents the stochastic Monte Carlo simulation (MCS) to assess the uncertainty of flow and conservative transport in 3D discrete fracture networks (DFNs). The MCS modeling workflow involves a number of developed modules, including a DFN generator, a DFN mesh generator, and a finite element model for solving steady-state flow and conservative transport in 3D DFN realizations. The verification of the transport model relies on the comparison of transport solutions obtained from HYDROGEOCHEM model and an analytical model. Based on 500 DFN realizations in the MCS, the study assesses the effects of fracture intensities on the variation of equivalent hydraulic conductivity and the exhibited behaviors of concentration breakthrough curves (BTCs) in fractured networks. Results of the MCS show high variations in head and Darcy velocity near the specified head boundaries. There is no clear stationary region obtained for the head variance. However, the transition zones of nonstationarity for x-direction Darcy velocity is obvious and the length of the transition zone is found to be close to the value of the mean fracture diameter for the DFN realizations. The MCS for DFN transport indicates that a small sampling volume in DFNs can lead to relatively high values of mean BTCs and BTC variations.