Molybdenite is associated with primary and secondary copper sulfide minerals. Few studies have focused on the selective flotation of molybdenite to separate it from secondary copper sulfide minerals, such as chalcocite. This study evaluated the use of oxidation treatment to separate molybdenite from chalcocite. The effects of oxidation treatment with hydrogen peroxide (H2O2) on the flotation behaviors of molybdenite and chalcocite in the presence of collectors (i.e., potassium amyl xanthate and diesel oil) were evaluated, and the impacts of H2O2 concentration, oxidation treatment duration, and pH level were assessed. Chalcocite flotation tests showed that the H2O2 treatment significantly reduced the recovery of chalcocite due to the formation of copper hydroxide and sulfate species on the chalcocite surface, which altered its surface hydrophobicity. On the other hand, the low surface oxidation of molybdenite led to high flotation recovery after the oxidation treatment. Oxidation treatment with a 10 mM H2O2 solution at a pH of 9 for 20 min resulted in a separation efficiency of 87%, with 98% molybdenite recovery and 11% chalcocite recovery. The results show that H2O2 oxidation treatment enables the selective flotation of molybdenite to separate it from chalcocite.