The 27-year-old, who had her first number one last year with Burn, took the trophy at Earl's Court in London four years after collecting her first.
Goulding, who beat Jessie J and Laura Marling to the prize said: "I genuinely am in shock. This means so much to me." Sheffield's Arctic Monkeys took the group and album awards, making it the third time they have carried off the double at the ceremony. Best group award went to France's Daft Punk.