In an interview with the Radio Times, the actress explained that she was surprised when viewers complained about an episode in which Amy tries to seduce the Doctor.
"[Being seductive is] part of who she is, but it's quite a small part," Gillan said. "She's a normal girl with normal impulses. I suppose I find it hard to define the relationship between Amy and the Doctor - I think we all do - because there are so many aspects to it."
However, Gillan admitted that she does not expect the pair to begin a romantic relationship.
"Ultimately, I think they're like brother and sister," she said. "He's quite protective of her and they bicker like siblings do, but ultimately they'd do anything for each other. Sometimes, though, she's attracted to him, and that's when things get a bit more complicated.
"I don't think he sees her like that at all. I think he basically still sees her as the little Amelia he met when she was 7. So when she kisses him, he's like, 'Ooh, this is all wrong', and she's like, 'Why isn't he reciprocating?' So she pushes it a bit, just to test her power. But in the morning, she's back to being his annoying little sister again."
Gillan also revealed that she has a good relationship with Matt Smith, who plays the Doctor.
"We just kind of bounce off each other," she said. "The banter that you see on screen - that's what we're like all day on set."
Doctor Who continues on Saturday at 6.40pm on BBC One.