Understanding the temporal evolution of fracture transport properties in shales is of increasing importance for the long-term safe operation of many underground engineering projects. Here, a series of long-term (60 days each) water seepage and gas breakthrough experiments utilizing three shale samples, each with a single artificial fracture, was conducted to evaluate the time-dependent evolution of permeability and gas breakthrough pressure (GBP) under constant confining stress. Our results show continuous decreases in permeability and increases in GBP with time, and the rate of change in both is initially rapid but then slows. As the loading time increases, the permeabilities and GBPs become relatively constant. The inferred mechanisms are aperture reductions caused by mechanical creep and clay swelling of fractures. Pretest and posttest scans of fracture surfaces reveal some changes in asperity height, which demonstrates the occurrence of mechanical damage to the fracture during the experiments. Long-term stress compaction causes flow channels to narrow or even partially close over time. The fluid flow in confined fracture is controlled by some narrow apertures in the flow channels, which act as bottleneck points. The apertures at these points decrease to the micro-nano level under stress, significantly reducing fracture transport properties. While the fracture transport properties of fractured shale obviously decrease during long-term stress compaction, residual fracture voids still dominate the fluid flow over a longer period, and are especially prone to gas escape.