In a statement from the Ministry of Foreign Affairs and International Cooperation in Lilongwe, Mutharika said: “On behalf of the Government and the People of the Republic of Malawi and indeed on my own behalf, I would like to extend my sincere and heartfelt congratulations to Your Honour, on your election as Prime Minister of the Great Britain.”
He said the election of Johnson manifests the confidence and trust that the people of the Great Britain have in him and that he hoped his ascendance to the higher office would further strengthen the friendly relations that exist between Malawi and Great Britain.
“May I take this opportunity to wish Your Honour personal good health and the well being of the people of the Great Britain,” he added.
Alexander Boris de Pfeffel Johnson has been elected new Conservative leader in a ballot of party members and has become the new UK prime minister, succeeding Theresa May who resigned some months ago over Brexit.
He beat Jeremy Hunt comfortably, winning 92,153 votes to his rival's 46,656.
In his victory speech, Johnson promised he would "deliver Brexit, unite the country and defeat Jeremy Corbyn".
Speaking at the Queen Elizabeth II centre in London, he said: "We are going to energise the country.
"We are going to get Brexit done on 31 October and take advantage of all the opportunities it will bring with a new spirit of can do.
"We are once again going to believe in ourselves, and like some slumbering giant we are going to rise and ping off the guy ropes of self doubt and negativity."
Johnson thanked his predecessor, saying it had been "a privilege to serve in her cabinet". He was May's foreign secretary until resigning over Brexit.
The outgoing PM - who is standing down after a revolt by Conservative MPs over her Brexit policy - congratulated her successor, promising him her "full support from the backbenches".
Foreign Secretary Hunt said he was "very disappointed", but Johnson would do "a great job". He said he had "total, unshakeable confidence in our country" and that was a valuable quality at such a challenging time.
Hunt added: "It was always going to be uphill for us because I was someone who voted Remain and I think lots of party members felt that this was a moment when you just had to have someone who voted for Brexit in the referendum.
"In retrospect, that was a hurdle we were never able to overcome."
Donald Trump told an event in Washington "a really good man is going to be the prime minister of the UK now," and Mr Johnson would "get it done", referring to Brexit.
The president added: "They call him Britain Trump. That's a good thing."
Almost 160,000 Conservative members were eligible to vote in the contest and turnout was 87.4%.
Johnson's share of the vote - 66.4% - was slightly lower than that garnered by David Cameron in the 2005 Tory leadership election (67.6%).