Anna Kepner’s 16-year-old stepbrother raped her before he murdered her on their family cruise vacation, the feds alleged for the first time Monday while charging him as an adult.

The boy, only identified as T.H. in charging documents, is facing life in prison for allegedly strangling his 18-year-old stepsister on the Carnival Cruise ship Horizon in November and stuffing her body under the bed in a room they shared.

The suspect in February was first charged as a juvenile for killing his cheerleader stepsister.

He has now been indicted by a federal grand jury for first-degree murder as well as aggravated sexual assault, the Department of Justice announced, while still referring to him only as “T.H., a minor,” despite charging him as an adult.

The 16-year-old, who reportedly had a twisted obsession with the high school senior, “sexually assaulted and intentionally killed” Kepner, the DOJ said.

He forced Kepner to “engage in a sexual act” and penetrated her, the superseding indictment alleges.

Kepner died from mechanical asphyxiation after her stepbrother held her in a bar hold, officials previously ruled.

Kepner’s younger brother ended up sleeping just feet away from his sister’s lifeless body.

Her body was found the morning of Nov. 7,  wrapped in a blanket, covered in life jackets, and shoved under a bed by a maid who was cleaning the cabin while on a six-day Caribbean cruise.

After the grisly discovery, the ship made a beeline for the Port of Miami.

Kepner — known affectionately by her family as “Anna Banana” — was set to graduate from Temple Christian School in Titusville in May.

The gymnast and cheerleader had just finished her test to join the military, her family said.