Carole Hudson, who has been chief executive of St Helens MBC since 1991, will stand down in March.
A successor is due to be appointed on 14 January for Ms Hudson who was an assistant chief executive for finance at St Helens before taking the top job.
Leader Barrie Grunewald (Lab) said: “I would like to thank Carole for her loyal service to the council and the people of St Helens and for her contribution towards the economic transformation of the borough.
“The last four years have been extremely challenging during the austerity programme and she has worked hard alongside our politicians to manage the council well, having to make significant budget cuts and at the same time ensuring that the council can continue to deliver its statutory responsibilities. I wish her well in her retirement.”
Meanwhile, Boston BC chief executive Richard Harbord has resigned citing family reasons.
He will represent the council at certain key meetings over the next few months but deputy Phil Drury will step up temporarily.
A council spokesman said a decision on filling the postilion long term was expected after all-out elections in May.