Police were called to a house in Droitwich, Worcestershire, on 18 February last year where Alfie Steele was found in a critical condition.
He was flown by air ambulance to hospital in Birmingham where he died.
Carla Scott, 34, and Dirk Howell, 39, are due to appear at Worcester Crown Court on 25 February for a plea and trial preparation hearing.
Ms Scott, from Vashon Drive, Droitwich, and Mr Howell, of Princip Street, Birmingham, have also been charged with causing or allowing the death of a child.
They also each face a charge of cruelty to a person aged under 16 between 13 July 2019 and 18 February 2021.
