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Chief executive and co-founder Ryan Baker was thrilled to win the award, quipping it was ''nine times lucky''.
Timely had been a finalist for five consecutive years and, before that, BookIt - another business two of the Timely founders were involved with - had been four times.
''It's been a long process and I think that kind of makes it even more rewarding,'' Mr Baker said.
The award was accepted by co-founder Will Berger at a function in Auckland on Friday night attended by about 900 people.
Timely produces a cloud-based appointment management system for businesses requiring scheduling of their staff and services.
The company was founded in 2012 by Andrew Schofield, Mr Berger and Mr Baker.
Mr Baker and Mr Schofield were previously involved in BookIt, an online software provider for tourism operators which was sold to Trade Me in 2010.
BookIt was initially developed by Mr Schofield, and Dunedin businessman Ian Taylor later bought into it.
They were later joined by Mr Berger, whom they met at Trade Me, and the trio started building Timely in March 2012, launching in July that year.
Yesterday, Mr Baker acknowledged Mr Taylor - who was inducted into the New Zealand Hi-Tech Hall of Fame in 2008 - saying they would not be doing what they were doing had he not ''backed a kid from Manapouri''.
Mr Schofield drove from Manapouri when he was 18 and turned up at Mr Taylor's office to show him the booking system he was making.
Mr Taylor gave him a job on the spot.
That turned into BookIt, which was later acquired by Trade Me, and Timely was spun out of that.
Mr Taylor had that trust in them and backed them. He had done a lot of good things for Dunedin, Mr Baker said.
Last year, Timely made the 2016 Deloitte Technology Fast 500 Asia-Pacific Index, coming 71st out of 500 with 770% growth in that last year.
Mr Baker was very proud of his team, which had grown to 38. About 15 had been employed in the past nine months or so. Head of sales Israel Butson had moved to Melbourne and opened an office.
The company was looking at global expansion and what opportunities there were, he said.
Judges said the calibre of this year's entrants was an ''all time high'' making the job of selecting winners exceedingly challenging.
More than 50 local and international judges assessed entrants across the 13 award categories.
PwC Hi-Tech Company of the Year was won by Pushpay. Judges said the company was the first to recognise a global unserved market need - credit and collections help for churches and charities.
Queenstown-founded Shotover Camera Systems, which developed the world's first gyro-stabilised camera system for shooting aerial footage in ultra high-definition, won best hi-tech solution for the creative sector.