Direct proof of use
The MQ-9 Reaper is directly documented in the 2001 War in Afghanistan through U.S. Air Force reporting from Kandahar Airfield. A December 2018 DVIDS story by the 455th Air Expeditionary Wing states that the 62nd Expeditionary Attack Squadron at Kandahar operated MQ-9s for deliberate strikes, close air support, and aerial reconnaissance, and identifies Afghanistan as the mission area.
A separate U.S. Air Force fact-sheet image caption places an MQ-9 Reaper assigned to the 62nd Expeditionary Reconnaissance Squadron on the Kandahar Airfield flightline on February 22, 2018. The aircraft was armed with four GBU-38 Joint Direct Attack Munitions before a mission, and the caption says the squadron provided close air support, intelligence, surveillance, and reconnaissance capabilities in Afghanistan.
Sources: DVIDS MQ-9 Keeps Eyes on Targets, USAF JDAM Fact Sheet
Timeline
The clearest public post-2015 Afghanistan evidence in this record comes from 2018. On February 22, an MQ-9 at Kandahar Airfield was photographed armed with four GBU-38 JDAMs before a mission. On December 2, DVIDS published a Kandahar-datelined report describing the local MQ-9 force's close-air-support, strike, and reconnaissance work.
The December 2018 report also describes the launch-and-recovery split that shaped MQ-9 operations in Afghanistan. Kandahar crews handled the line-of-sight takeoff and landing phases, then handed aircraft control to stateside mission crews once the aircraft was above the local phase of flight.
Sources: USAF JDAM Fact Sheet, DVIDS MQ-9 Keeps Eyes on Targets
Operational role
The documented operator was the U.S. Air Force within the U.S.-led, NATO, and Afghan-government-aligned side of the war. The cited sources support fielding from Kandahar Airfield during Operation Freedom's Sentinel and NATO Resolute Support-era operations, not Afghan government possession of the aircraft.
The supported role was armed persistent ISR with the ability to support ground forces through close air support and deliberate strikes. The DVIDS account describes long-duration missions, onboard camera-sensor work, intelligence, surveillance, and reconnaissance, and the aircraft's impact on troops on the ground. The Air Force caption adds a weapon-load example by identifying four GBU-38 JDAMs on a Kandahar-based MQ-9 before a mission.
Sources: DVIDS MQ-9 Keeps Eyes on Targets, USAF JDAM Fact Sheet