The chain's chief executive Jo Boydell apologised to the victim in a statement on Sunday and said the changes would ensure additional or replacement keys were only issued with permission from the person staying in the room.
"We got things wrong and we should have acted sooner and I am truly sorry for that," she said.
Prior to Boyden's statement, the victim, who wishes to stay anonymous, told the BBC that Travelodge had "ample opportunity to deal with the case better" but "took a very long time to reply to me and didn't really take it very seriously".
"It was escalated in their company a little bit... but they still didn't take the right precautions to deal with the situation," she said.
Travelodge initially offered the victim a £30 refund, which she described as "insulting", before the company issued an apology.
Ros Tappendenand, Alex Meakin, South of England