Waddington, European social media and digital director at Ketchum Pleon, beat academic Dr Jon White to the role with 68 per cent of the vote.
He will step in as president next January, replacing Sue Wolstenholme.
Waddington’s victory follows an election re-run after the result of a previous vote for the role was scrapped in November.
Waddington said: ‘The CIPR as the professional body representing public relations in the UK and further afield stands at a moment in time. We have a real opportunity to assert our value as a management discipline that enables organisations to engage in a two-way conversation, and ultimately a relationship, with audiences both internal and external. We also have the opportunity to improve the reputation of our industry via professional development.
‘Huge thanks to Dr Jon White for a contest worthy of the opportunity that our profession faces, and to everyone that got behind my campaign. The hard work starts now.’
Rules for the election were changed after Lionel Zetter, who was voted into the role, had to stand down when it emerged that his nomination was accepted despite being submitted after the CIPR’s deadline.
The changes included allowing any voting member of the CIPR to run for the role if they were nominated by 10 other members.
CIPR CEO Jane Wilson commented: ‘Of the two high quality candidates, Stephen is a superb choice and I know he will lead the CIPR very effectively in championing the public relations profession, advancing professional standards and engaging with CIPR members on a national and international scale.
'It has been a pleasure to work with Stephen already on CIPR Board and he will bring great enthusiasm and commitment to the role of president elect, becoming president in 2014. I wish him every success.’
Waddington currently serves on the CIPR executive board and is chairman of the organisation's Policy and Campaigns Committee.