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. Lipnitskaya selected all the music for her programs by herself. For the 2013–14 season, she chose Mark Minkov's "You Don't Give Up On Love" (Russian: "Не отрекаются, любя") for her short program, because she loves the song. She chose the theme from "Schindler's List" for her free skate after she had watched the film many times. Initially, her coach was not convinced that it was a good idea and they struggled to find a choreographer for the program. Former ice dancer Ilia Averbukh choreographed her programs. Coach Eteri Tutberidze said: "She had repeatedly watched this movie – and she said she wanted to be the girl in the red coat". In the 2013–14 season, Lipnitskaya became age-eligible for all senior ISU events. She began her season by winning the gold medal at the 2013 Finlandia Trophy. Her first 2013–14 Grand Prix event was the 2013 Skate Canada International. She placed second in the short program and first in the free skate, winning gold with 198.23 points in total. She won another gold medal at the 2013 Rostelecom Cup with a new personal best SP score of 72.24 points. The results qualified her to the Grand Prix Final. At the event in Fukuoka, Japan, she placed fourth in the short program, second in the free skate, and won the silver medal behind Mao Asada. She is Russia's youngest medalist at the Final since Irina Slutskaya. Lipnitskaya won the silver medal behind Adelina Sotnikova at the 2014 Russian Championships, after placing second in the short and first in the free. In her European Championships debut, she placed second to Sotnikova in the short program, first in the free skate, and scored a total of 209.72 points (the first Russian to score above the 200 mark in ladies' singles).