The software giant posted a $4.7bn (£3.8bn) profit for the three months to September.
Chief executive Satya Nadella has focused on building Microsoft's expertise in cloud-based services amid slowing PC sales.
Shares rose 6% to $60.73 in after-hours trading.
The previous high was $59.97 in December 1999, close to the peak of the dot-com boom, shortly before Steve Ballmer replaced Bill Gates as chief executive.
When Mr Nadella succeeded Mr Ballmer in 2014, Microsoft's shares were trading below $37.