The Forest of Dean MP and former accountant takes the role from Anne-Marie Trevelyan, who was appointed at the start of September by former prime minister Liz Truss.
Harper previously backed Sunak in his bid to become prime minister and was chief whip at the end of David Cameron’s premiership.
He also chaired the Covid Recovery Group of Conservative MPs – a group that was against lockdown restrictions – and backed the remain campaign during the 2016 EU referendum.
Speaking on his new role, Harper said via Twitter: "Delighted to be appointed secretary of state for transport by prime minister Rishi Sunak. Transport affects us all, and I can’t wait to tackle the challenges we face so we can deliver for communities across our United Kingdom."
Trevelyan also took to Twitter and said: "Congratulations to [Mark Harper] on his appointment as transport secretary – continuing to deliver on our 2019 manifesto, building infrastructure to help us level-up the whole of the country, and driving the net zero revolution."
Clive Wratten, chief executive of the Business Travel Association (BTA), welcomed the new appointment.
"We look forward to working in close collaboration to further the growth of the UK’s infrastructure, and the promotion of aviation for British business and international trade," he added.
"This is a vital time for businesses of all sizes, and we need a period of stability in order to grow confidence in business travel once more."
