The 58-year-old school principal from Dublin won 144 out of a possible 278 votes and was 98 ahead of his nearest rivals Sean Walsh and Frank Burke.
Horan will take over from current president Aogan O Fearghail in 2018.
"Aogan is the president for the next 12 months so I'll support him and learn from him as best I can," said Horan at Croke Park.
The other candidates for the post were Martin Skelly with 22 votes while 20 went to Robert Frost.
This weekend's annual congress will be dominated by new championship proposals in football and hurling.
The plans put forward by GAA director general Paraic Duffy include completing the All-Ireland Senior Championships by the end of August.
Also included is a new round-robin format for the All-Ireland SFC quarter-finals, which would mean more games.
This proposal has proved particularly controversial in recent weeks.
Both the Gaelic Players' Association and recently formed Club Players' Association have come out against Duffy's plans, although not necessarily for the same reasons.
Ostensibly, the main reason for these mooted changes is to try and ensure more regular games for club players but there is a certain  amount of bafflement as to how this can be squared with the motion to have a round-robin stage in the All-Ireland Football quarter-finals.
The new club players' body has been angered after the GAA's top brass refused to grant it a speaking platform at the Croke Park gathering.
However, that may change at further annual gatherings of GAA delegates if a motion for the club players' body to be officially recognised is passed in Dublin.
All the indications are that the votes on both the so-called new 'Super Eight football round' and the proposal to bring forward the All-Ireland finals will be exceptionally close, with a two-thirds' majority required for the format changes to be tried for a three-year period.
To make matters even complicated, congress will also hear a number of motions calls from the two-thirds majority to be scrapped, with one call suggestion a simple majority and another calling for the figure to be lowered to 60%.
Inevitably, those motions will require a two-thirds majority to be passed.
Going into the weekend, Croke Park's desire for replays to be scrapped - in favour of extra-time - in all championship games bar provincial and All-Ireland finals looks likely to be comfortably passed.
At last year's congress, motions to move All-Ireland Finals to earlier in the year and scrap replays were both defeated, although the finals proposal fell narrowly short after getting support from 60.8% of delegates.
John Horan easily won the vote at Congress on Friday night to become the GAA president-elect.