Pompeo, who was confirmed by the Senate by 66-32 votes, replaces John Brennan, a political appointee, whose term ended on January 20 with that of Barack Obama as the US President.
Later, Pompeo was sworn in last night as CIA director.
"You are stepping up to lead the finest intelligence- gathering operation the world has ever seen," Vice President Mike Pence said during the swearing-in ceremony.
Significantly, Trump, who succeeded Obama as the 45th President of the US, made his first visit to a federal agency to CIA headquarters in Langley.
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Pompeo, 53, is only the third member of Trump's cabinet to take his post after Secretary of Defence James Mattis and Homeland Security Secretary John Kelly were sworn in Friday.
On Pompeo's conformation, Senator John McCain, in a statement, said the new Director of the CIA must focus on uncovering facts about the many complex national security threats confronting the nation.
Congressman Davin Nunes, Chairman of the House Permanent Select Committee on Intelligence, said Pompeo with his deep background in intelligence and military affairs, he is confident will serve the intelligence community well and make vital contributions to national security.
"At a time when Americans face escalating threats from both terror groups and state entities, it's reassuring that someone with as much experience and knowledge as Mike will be leading one of the nation's premier intelligence agencies," he said.
This has paved the way for the Senate to formally vote on his nomination following which Tillerson would occupy the Foggy Bottom headquarters of the State Department as the top American diplomat.
The position has been vacant since January 20 when John Kerry's term demitted office with outgoing president Obama.
Even as Trump had nominated Tillerson as his Secretary of State much in advance, the Senate has not been able to confirm him because of some reservations by a few lawmakers, including from Trump's own Republican party.
"I personally have no doubt that Rex Tillerson is well-qualified. He's managed the world's eighth largest company by revenue with over 75,000 employees," said Senator Bob Corker, Chairman of the Senate Foreign Relations Committee.
"Diplomacy has been a critical component of his positions in the past, and he has shown himself to be an exceptionally able and successful negotiator who has maintained deep relationships around the world," he said.
Announcing his support for Tillerson, Rubio said he believes the President is entitled to significant deference when it comes to his choices for the cabinet.
"I also believe given the uncertainty surrounding the future direction of our foreign policy that a higher degree of scrutiny is justified in evaluating whoever is nominated to serve as secretary of state," Rubio said.
"Given Mr Tillerson's history of taking Putin's side against US interests, the Kremlin could not have asked for a better Secretary of State," he said.
Congratulating Pompeo on his confirmation, Senator Mark R Warner, Vice Chairman of the Senate Select Committee on Intelligence, said, "I believe that he can be an effective leader of the CIA at a time when the Agency is facing many challenges."
"While I do not agree with some of the views he has expressed, Congressman Pompeo has impressed me with his respect for the dedication and impartiality of the intelligence professionals at the CIA," Warner said.
"America needs a CIA director who will uphold American values by resolutely condemning torture and mass surveillance. Congressman Pompeo's last minute attempt to walk back his opposition to torture is very disturbing, and suggests the Trump Administration is readying to abandon our commitment to international human rights," he said.
Pompeo was a member of the US House of Representatives from 2011 to 2017.