A consultation launched in October has finished and the firm confirmed it would cut staff numbers by about 25% at its Worksop offices and supply chain.
A spokesman said the changes were being made so it could "react quickly to the fast moving retail environment".
The business faced a "challenging" situation but was "financially robust", he added.
The chain, which started with a single shop in 1930, has more than 370 stores across the UK.
It employs about 23,000 staff and has annual sales of more than Â£1.5bn.
Up to 170 jobs are to go at high street retailer Wilko's headquarters in Nottinghamshire.