Lipnitskaya qualified for the Grand Prix Final in Sochi, Russia, but withdrew due to injury — during training on 28 November, she lost balance on the entry to a spin, split her chin and sustained a slight concussion. Doctors recommended that she stay off the ice for at least two weeks. She resumed partial training in mid-December, omitting jumps and spins, and then after eight days began full training. Needing more preparation time, Lipnitskaya withdrew from the senior Russian Championships. She returned to competition at the 2013 Russian Junior Championships and finished in 5th place. After the competition, Lipnitskaya said she was still working to return to form after her injury and puberty issues. She then competed at the 2013 World Junior Championships where she won the silver medal with teammates Elena Radionova and Anna Pogorilaya taking the gold and bronze medals respectively.