Low pressure‐high temperature (LPHT) metamorphism, with geothermal gradients in the order of 50–100°C/km, is a common feature of the late evolution of collisional orogens. These abnormal thermal conditions may be the results of complex interactions between magmatism, metamorphism and deformation. The Agly massif, in the French Pyrenees, preserves the metamorphic footprints of the late Variscan thermal structure of an almost continuous section from the upper and middle continental crust. The upper crust is characterized by a very high geothermal gradient of ~55°C/km, evolving from greenschist to amphibolite facies, while the middle crust, exposed in a gneissic core, exhibits granulite facies conditions with a near isothermal geothermal gradient (<8°C/km) between 740 and 790°C. The abnormal and discontinuous crustal geothermal gradient, dated at c. 305 Ma on syn‐granulitic monazite by LA‐ICP‐MS, is interpreted to be the result of magmatic intrusions at different structural levels in the crust: the Ansignan charnockite (c. 305 Ma) in the deepest part of the gneissic core, the Tournefort granodiorite (c. 308 Ma) at the interface between the gneissic core and the upper crust and the Saint‐Arnac granite (c. 304 Ma) in the upper section of the massif. The heat input from these magmas combined with the thermal buffering effect of the biotite dehydration‐melting reaction resulted in the near isothermal geothermal gradient in the gneissic core (melt‐enhanced geotherm). The higher geothermal gradient (>50°C/km) in the upper crust is only due to conduction between the hot middle crust and the Earth's surface. The estimated maximum finite pressure range suggests that ~10 to 12 km of crust are exposed in the Agly massif while the present‐day thickness does not exceed 5–6 km. This pressure/depth gap is consistent with the presence of several normal mylonitic shear zones that could have contributed to the subtraction of ~5 km of the rock pile. Monazite U–Th–Pb ages carried out on monazite overgrowths from a highly mylonitized sample suggest that this vertical thinning of the massif occurred at c. 296–300 Ma. This later Variscan extension might have slightly perturbed the 305 Ma geothermal gradient, resulting in an apparent higher conductive geothermal gradient in the upper crust. Although the Agly massif has been affected by Cretaceous extension and Eocene Alpine compression, we suggest that most of the present‐day thickness of the column rock was acquired by the end of the Palaeozoic.