Rutte's appointment became a formality after his only rival for the post, Romanian President Klaus Iohannis, announced last week that he had quit the race, having failed to gain traction.
Rutte will take over on October 1 from Jens Stoltenberg of Norway, who is stepping down after a decade in the post.
Ambassadors from the alliance's 32 members took the decision at a meeting at NATO headquarters in Brussels on Wednesday.
Rutte said he looked forward to taking up the job "with great vigour".
It is a tremendous honour to be appointed Secretary-General of NATO. The Alliance is and will remain the cornerstone of our collective security. Leading this organisation is a responsibility I do not take lightly. I'm grateful to all the Allies for placing their trust in me. I…— Mark Rutte (@MinPres) June 26, 2024
"The Alliance is and will remain the cornerstone of our collective security. Leading this organisation is a responsibility I do not take lightly," he posted on X.
After declaring his interest in the post last year, Rutte gained early support from key members of the alliance including the United States, Britain, France and Germany.
Others were more reticent, particularly Eastern European countries which argued the post should go to someone from their region for the first time.
But they ultimately rowed in behind Rutte, a fierce critic of Russian President Vladimir Putin and a staunch ally of Ukraine.
Stoltenberg said he warmly welcomed the selection of Rutte as his successor.
I warmly welcome — Jens Stoltenberg (@jensstoltenberg) #NATO Allies' choice of @MinPres Mark Rutte as my successor. Mark is a true transatlanticist, a strong leader and a consensus-builder. I wish him every success as we continue to strengthen NATO.I know I am leaving NATO in good hands.https://t.co/D0ass7fKiLJune 26, 2024
"Mark is a true transatlanticist, a strong leader, and a consensus-builder," he said.
"I know I am leaving NATO in good hands."
NATO takes decisions by consensus so Rutte, who is bowing out of Dutch politics after nearly 14 years as prime minister, could only be confirmed once all 32 alliance members gave him their backing.
Rutte will face the challenge of sustaining allies' support for Ukraine's fight against Russia's invasion while guarding against NATO's being drawn directly into a war with Moscow.
He will also have to contend with the possibility that NATO-sceptic Donald Trump may return to the White House after November's U.S. presidential election.
Trump's possible return has unnerved NATO leaders as the Republican former president called into question US willingness to support other members of the alliance if they were attacked.
