Her movie Ratcatcher, about a young boy's escape from a grim Glasgow tenement when he discovers a new housing estate on the edge of the city, took the British Film Institute's Sutherland Award.
The title goes to the most original and imaginative first feature screened during the festival.
Ms Ramsay's film - released on Friday, 12 November - was the only British film on a shortlist of 10, all of which have been shown during the two-week festival.
London Film Festival director Adrian Wootton said: "It is a mesmerising achievement with a real poetic vision."
A gala performance of Ratcatcher launched the 53rd Edinburgh International Film Festival in August.
The event marked the first time the opening slot had been taken by a Scottish film for 15 years.
Scottish talent
The emphasis on home-grown talent and local heroes reflected a new consciousness and pride, brought about by devolution and the new Scottish Parliament.
The film is set in the mid Seventies, during Glasgow¿s dustman strike, on a severely crumbling estate of council flats.
The film centres on one family, and particularly 12-year-old James, who is played by William Eadie.
After a tragic start to the film, he becomes more and more alienated from the world and people around him.
The new housing estate his family wants to be transferred to - complete with brilliant sunshine and idyllic cornfield location - is in stark contrast to the deteriorating landscape of the rubbish-strewn housing estate.
The film also stars: Tommy Flanagan, Mandy Matthews, Michelle Stewart, Lynne Ramsay Jnr, Leanne Mullen and John Miller.