The actress, who plays Amy Pond, revealed on The One Show that the pair had to just get on with their on-screen embrace.
When asked how they went about the scene, Smith replied: "We just said let's go for it."
Gillan added: "I just sort of planted one on him."
Presenter Alex Jones then asked Gillan if she enjoyed it, to which the star replied: "Not initially, no."
Smith previously said that Gillan's character was "the sexiest companion ever".