As a stalwart defender for the Lionesses, Stoney earned 130 caps and represented England at three FIFA Women’s World Cups and three UEFA Women’s European Championships. She also captained Team Great Britain during the London 2012 Olympic Games and was twice named in the Professional Football Association (PFA)’s Women’s Team of the Year. Her distinguished leadership on and off the pitch earned her an appointment as a Member of the Order of the British Empire (MBE) - an honour that was announced while Stoney was part of the England squad competing at the 2015 FIFA Women’s World Cup in Canada.

Transitioning to coaching, Stoney made her debut at Chelsea in 2009 while still an active player, serving in the role of player-manager. Immediately following her retirement in 2018, Stoney joined the staff of the England Women’s National Team as an assistant under Phil Neville before being hired as the inaugural head coach of Manchester United Women. Stoney led Manchester United to the FA Championship title in their debut season, earning promotion and establishing them as a competitive force in the Women’s Super League. Stoney also completed her UEFA Pro License while at Manchester United.

In 2021, Stoney was named the first head coach of the expansion San Diego Wave FC in the National Women’s Soccer League (NWSL). In its debut season, in 2022, Wave FC finished third in the NWSL table and reached the playoff semi-finals before losing to the eventual champion Portland Thorns. Stoney earned 2022 NWSL Coach of the Year honours, while in the same year coaching Canada Soccer's Women’s National Team standout Kailen Sheridan to NWSL Goalkeeper of the Year. In 2023, Stoney cemented Wave FC as a top performing club in the league in only its second year as a franchise, as they finished first in the NWSL table and captured the NWSL Shield. Stoney also coached Wave FC to a NWSL Challenge Cup victory to begin the 2024 season.