The politician, who had secured his 2011 seat through the list vote, beat SNP candidate rival Roderick Campbell by 3,465 votes.
Mr Rennie received 14,928 votes, an increase of 15% from 2011.
He said: "It feels fantastic to have won North East Fife back for the Liberal Democrats. A big majority of 3,000 against a Nationalist tide."
Mr Rennie added: "It's a tremendous result for the Liberal Democrats in North East Fife."
In his victory speech, he said it had been a "positive, uplifting campaign" and added: "I've had the time of my life in this campaign."
He appeared at the count with two toy pigs in his hand, a reference to a photo opportunity at farm while out on the campaign trail.
Alex Cole-Hamilton, of the Liberal Democrats, also won Edinburgh Western from the SNP, with 16,645 votes - a 42% share.
The party also comfortably held both Orkney and Shetland.
Scottish Liberal Democrat leader Willie Rennie has taken the Fife North East seat from the SNP.