Khalil is the member of parliament representing the Marjeyoun/Hasbaya district. He is part of the Amal Movement led by Parliament Speaker Nabih Berri which is part of the opposition. He is a senior aide to Berri. Khalil was appointed minister of public health in the cabinet of Najib Mikati on 13 June 2011. Khalil's term ended when he was appointed minister of finance, replacing Mohammad Safadi in the post.