Luna offers to carry Pigwidgeon’s cage as the group prepare to leave their compartment, and carries the owl off the Hogwarts Express, joining the others outside Hogsmeade Station. Luna tells Harry that, although the others cannot, she is also able to see the skeletal horses that pull the Hogwarts carriages, and has been able to since her first day at Hogwarts. She reassures Harry that he is as sane as she is. Luna enters the carriage after Ron, Hermione and Ginny for the journey to the castle.
Luna trails behind the rest of the fourth-year Herbology class, a smudge of earth on her nose. When she sees Harry she heads straight towards him, and tells him that she believes He-Who-Must-Not-Be-Named has returned, and that Harry fought and escaped from him the previous year. She gives Hermione a withering look and flounces away when Hermione disagrees with her justification that once, people didn't believe creatures like the Blibbering Humdinger existed either.
Luna goes with Harry, Ron, Hermione, Ginny and Neville to the Department of Mysteries. Once in the main hall of the department, the group try to find the correct door to lead them to the place where Harry saw Sirius lying injured.
Luna is excited when she sees a large tank of what she believes are Aquavirius Maggots, which her father believes the Ministry are breeding, but on closer inspection it is a tank of brains. In the room with the veiled archway, Luna tells Harry that she too can hear voices coming from behind the veil, and believes there are people behind it.
When the group enter the Time Room, they follow Harry as he leads them towards a second door. Once through, they creep through the cold room towards row ninety-seven, confused when Sirius is nowhere to be found. The group are surprised when Ron finds a glass orb with Harry's name on it in.
Luna and the other students in the Department of Mysteries fight against the Death Eaters. She is hit with a spell by one of the Death Eaters in the Brain Room and goes flying through the air, hitting a desk and sliding over its surface onto the floor, unconscious.
Luna attends Professor Slughorn's party with Harry wearing a set of spangled silver robes. She talks briefly with Professor Trelawney, and tells her that she has Firenze as her Divination teacher this year. Luna tells Harry that she doesn't think he should become an Auror, as she believes they are part of the Rotfang Conspiracy; a group working within the Ministry working to bring the institution down using a combination of Dark magic and gum disease.
Luna attends the funeral of Professor Dumbledore. She helps the recuperating Neville into his seat. Harry believes that Neville and Luna were the only people to respond to Hermione's summons the night Dumbledore died because they were the two who missed the DA most, and checked their coins regularly in the hope of another meeting.
Luna attends Bill and Fleur's wedding with her father, Xenophilius. She wears bright yellow robes and a sunflower in her hair. Luna recognises Harry immediately, despite his disguise, saying she recognised his expression.
Luna attends Dobby's funeral at Shell Cottage, huddled in one of Fleur's coats. She closes Dobby's eyelids, so that it looks as though he is sleeping. After Dobby is placed in the grave, Luna announces that she thinks they should say something. She thanks Dobby for rescuing her from the cellar at Malfoy Manor, and thinks it unfair that he had to die when he was so good and brave. She and the others leave Harry alone at the grave after the funeral.