As part of the project, a night-time road closure will be in place from 7pm to 6am each weekday.
The improvements will be carried out in phases, with works taking place at one roundabout leg at a time.
Advanced signage will be in place notifying road users which leg is currently being worked on.
The diversion route for the east and west A631 legs will be via A15 / A1500 / A156 / A631, and vice versa.
The diversion for the north and south B1398 legs will be via A631 / A15 / B1205 / B1398, and vice versa.
Karen Cassar, assistant director of highways, said: "As part of these works, we will be rebuilding sections of the A631 Harpswell Roundabout that are nearing the end of their serviceable life.
"This will involve removing the current carriageway and replacing it with 3,300 tonnes of tarmac and other road materials.
"We'll be doing everything we can to keep disruption to a minimum, including carrying the works out overnight so people using it in the day aren't affected by the works, as well as only closing one leg of the roundabout at a time.
"Once complete, these improvements will make travelling the A631 much safer and more comfortable for all road users."
For up-to-date information about this and other roadworks, visit www.lincolnshire.gov.uk/roadworks.