Gaines beat out fellow finalists Rio Tinto Dampier Salt general manager Brendon Brodie-Hall and Thiess senior advisor, diversity, inclusion and community Nevinia Davenport.
"We want to ensure as many women as possible have the opportunity to participate and make a strong contribution to Australia's resources sector and challenge the perception that mining is a male-dominated industry," Gaines said on Friday ahead of her win.
"Diversity isn't just the right thing to do, it is the smart thing to do and it is time to change the conversation around diversity from asking ‘why' to asking ‘how'.
"Fortescue is proud to be leading the charge by building strong talent pools of women, creating a culture which supports diversity through the implementation of practical initiatives to support parents in the workplace and encouraging leadership development for female team members."
The Outstanding Woman in Resources for 2020 was Chevron Australia Aboriginal employment stategy manager Rishelle Hume.
The other finalists were Metisphere managing director Ali Burston, CSA Global principal consultant Ivy Chen, and Trigg Mining MD Keren Paterson.
Woodside Energy system engineer Vanessa Bullock was named Outstanding Young Women in Resources, Chevron's Polly Mahapatra and Rio's Kathryn Serjeantson.
Newmont Australia haul truck operator Jennifer Ward was Outstanding Operator/Technician/Trade Woman in Resources over BHP's Allison Fuller and FMG's Briohny Evans.
Compass Group's Launch into Work program won the Outstanding Company Initiative for the large companies, over BHP's indigenous development program and Rio's Busting the Myth of Merit program.
The small to medium company award went to BOAB for indigenous engagement, over Bis Industries' Girls Rocking Resources and Gold Fields' St Ives Diversity & Inclusion Group.
The awards were presented in Perth on Friday night.
CME chief executive Paul Everingham said the awards demonstrated the value of diversity and inclusion and the benefits it provided to both the employee and employer.
"WIRA allows us to acknowledge inspirational women working in Western Australia, the men and women who champion gender diversity and the efforts made by companies in the sector to improve the participation of women in our workforce," he said.
"It was an honour to be surrounded by some of our current and future leaders in mining and energy, who represent the strong contribution and enormous value diversity and inclusion bring to our sector.
"We need to create positive environments where individuals feel comfortable to express their diversity of experiences and thought and where organisations can both listen and leverage that diversity. Diversity leads to better discussions, decisions and outcomes for everyone."