The analysis of geothermal energy storage in underground reservoirs relies on understanding non-isothermal fluid injection within fractured porous media through injection and production wells. Fluid flow, rock deformation, and heat transport are fundamental for assessing the stability and efficiency of storage in underground structures. Simulating these phenomena along the fracture network requires high computational effort if fractures are explicitly modelled. Because boundary conditions are often only measurable at the surface, accurate modeling also requires approach that accounts for hydraulic head losses and the thermal properties of the fluids involved. This research presents a fully coupled finite element scheme designed to simulate the evolution of fluid pressure, temperature, and rock deformation in fractured reservoirs. To minimize computational effort and minimize mesh refinement issues, fractures are considered as lower-dimensional elements, with distinct stiffness and permeability, representing preferential flow paths in contrast to the low-permeability matrix. Injection and production wells are modeled as linear elements that represent pipelines with specific roughness and diameter. Our numerical framework is validated by comparing it with multirate mass transfer models and theoretical formulations, showing excellent agreement. The results reveal that hydraulic head losses along the wells and the evolution of fracture permeability—influenced by thermo-mechanical processes—are critical factors in determining flow rates under a fixed operational pressure. Ignoring these head losses can lead to errors in flow rate predictions of up to an order of magnitude, highlighting the model's importance for the design of geothermal energy operations. This approach offers a more efficient way to simulate coupled heat transport, fluid flow, rock deformation, fracture aperture and pipe flow processes, enhancing the realistic representation of geothermal energy storage in deep rock formations.