England
At junior level, Scott played for the England Under-19s side, scoring three times in three games as England won through the first round of qualifying for the 2006 UEFA Under-19s tournament. Her first call-up to the England senior squad came in May 2006, having captained the Under-19s side for the previous 18 months. She made her debut for the England senior team against the Netherlands in August 2006, coming on as a late substitute for Kelly Smith in a 4–0 win. She made the squad for the 2007 World Cup, coming on as a substitute in England's opening match against Japan. She went on to start the remainder of England's matches in the tournament, scoring her first international goal in the 6–1 demolition of Argentina in the group stage. England bowed out at the quarter-final stage after a 3–0 defeat against the United States.
In May 2009, Scott was one of the first 17 female players to be given central contracts by The Football Association. She was named in coach Hope Powell's squad for the 2009 UEFA Women's European Championships, scoring a late winner as England beat the Netherlands in the semi-final, having come on as a substitute for Jessica Clarke at the beginning of extra-time.
At the 2011 FIFA Women's World Cup, Scott scored against New Zealand in England's 2–1 group B win. She put England ahead against France in the quarter final, but did not take a penalty in her team's 3–4 shootout defeat following a 1–1 draw. In February 2019, Scott pulled out of the England squad for the SheBelieves Cup.
On 23 February 2021, Scott made her 150th appearance for the England team in a game against Northern Ireland, which she would captain and play the whole 90 minutes as England would win 6–0.
In June 2022, Scott was included in the England squad which won the UEFA Women's Euro 2022. On 23 August 2022, Scott announced her retirement from football, a day after England and Manchester City teammate Ellen White did. Scott retired as England's second-most capped international footballer (men and women), behind Fara Williams.
Scott was allotted 163 when the FA announced their legacy numbers scheme to honour the 50th anniversary of England's inaugural international.