In the Qarachilar Cu-Mo-Au deposit of the Ahar–Arasbaran metallogenic zone (AAMZ), northwest Iran, mineralization occurs as three quartz-sulfide veins that cut granodiorite-quartz monzodiorite rocks of the Qaradagh batholith (QDB). Ore formation can be divided into three stages, with chalcopyrite, molybdenite, and gold-bearing pyrite appearing mainly in the first two stages. The main wall-rock alteration is silicification, and intermediate argillic, carbonate, and propylitic alteration. Fluid inclusion microthermometry indicates trapping of medium- to high-salinity (9.2–55 wt% NaCl equiv.) fluids at Qarachilar. Fluid inclusion trapping conditions are estimated to be 190 °C–530 °C and 0.1–3 kbar. The variable phase ratios as well as spatial coexisting of liquid- and vapor-rich two-phase and halite-bearing multiphase fluid inclusions homogenizing over the same temperatures are consistent with fluid boiling during ore formation. Obtained δ¹⁸O_H2O values of quartz from ore-stage veins are +5.7‰ to +9.7‰, signifying that the ore–fluid system was predominantly magmatic water. The average calculated δ³⁴S_H2S values are 1 ± 1‰ for pyrite, chalcopyrite and molybdenite, consistent with a magmatic source for sulfur. Combined, the fluid inclusion and stable isotope data indicate that the ore-forming fluids at Qarachilar were magmatic in origin and were subsequently cooled and diluted by meteoric water. Fluid boiling and mixing facilitated hydrothermal alteration and mineralization. Molybdenite Re–Os dating shows that mineralization occurred at 42.35 ± 0.16 Ma, coincident with formation of porphyry Cu-Mo mineralization at Agarak deposit, and Hanqasar, Aygedzor and Dastakert prospects in the Lesser Caucasus. However, Qarachilar is older than all porphyry Cu-Mo mineralization in the AAMZ and Urumieh-Dokhtar magmatic arc (UDMA), which suggests that collision between Arabia and Eurasia were oblique and thus diachronous. Our data suggest that mineralization at Qarachilar is related to collisional Eocene magmatic–hydrothermal activity related to Neo-Tethys subduction, and shares a number of similarities with the vein-type Cu-Mo-Au mineralization related to Cu-Mo porphyries.