Trains will not serve Moorfields, Lime Street and Liverpool Central stations for six months during the "essential renewal works", Network Rail said.
Services will not operate beyond Birkenhead Central and Birkenhead North at certain times.
Alternative travel arrangements will run during the works.
Merseyrail managing director Jan Chaudhry Van der Velde said: "The work that Network Rail will undertake next year is essential for maintaining the safe and reliable operation of the infrastructure built in the 1970s.
"However, we do not underestimate the inconvenience this will cause to our Wirral line passengers in the short term."
Rail passengers travelling between Liverpool and Wirral are being warned of longer journey times when major engineering works begin in January.