Kelly was promoted to the new role after joining FFA as the Chief Financial Officer in January 2012. Previously, he spent a decade in senior executive roles with Ten Network Holdings.
During FFA's broadcast negotiations last year, Kelly played a leading role in securing arrangements that will deliver $160 million of economic value of the next four years.
FFA CEO David Gallop said the creation of the COO role and the appointment of Kelly were the first steps in a restructure aimed at giving FFA a greater focus on implementation of strategies and operational efficiency.
"John Kelly has vast experience in corporate finance and executive administration within the sports and entertainment industry," Gallop said.
"His significant role in the successful broadcast negotiations was acknowledged by all parties.
"In my first 100 days in the job John's sharp business and financial acumen have been demonstrated on a wide range of major projects beyond his finance portfolio.
"I'm delighted John has accepted this important role as COO and I look forward to working closely with him to make FFA a better organisation for all our stakeholders."
As COO, Kelly will retain responsibility for finance and assume control of international and domestic broadcast and digital rights, information and communications technology, major event acquisition and stadium hiring arrangements.
He will have a formal co-ordination role over major projects that cover a range of new business opportunities for the benefit of community football and the professional tier.
"I'm grateful to David Gallop for giving me this new opportunity and having confidence in my ability," Kelly said.
"My first year at FFA has given me a great insight to the football world. I'm tremendously excited by the growth I've seen this season and the opportunities ahead.
"As COO, I look forward to the challenge of delivering business improvements across a wide range of activities."