For the 2016–17 season, Lipnitskaya was assigned to two ISU Grand Prix events, Skate America and Rostelecom Cup. She began her season by placing second at the Ondrej Nepela Memorial, to teammate Maria Sotskova. Lipnitskaya withdrew from Skate America after a recurring injury.
She opted to compete at her second Grand Prix assignment, the 2016 Rostelecom Cup. In the short program, Lipnitskaya earned a 69.25, the highest score she's received since the 2014 Cup of China, and she went into third place behind compatriots Elena Radionova and Anna Pogorilaya who placed second and first respectively.