It is believed 15 jobs will be lost when the store, one of the major units in the Hildreds Centre, shuts its doors on June 11.
The Skegness store is one of 16 nationwide set to close this year, with a total job loss of 330 jobs.
As well as Skegness, affected stores include Bournemouth, Stockton, The Fort, Shipley, Scunthorpe ,Narborough Road, Grantham, Redditch, Rotherham, Sutton, Coldfield, Orpington, Edmonton Green, Llanelli, Merthyr Tydfil and Cleethorpes.
Each store will have a 30-day consultation period, while permanent recruitment in the vicinity of each site will freeze.
Lincolnshire World reached out to the company about the decision.
We were told that Wilko had, with regret, briefed its team members in Skegness of the decision and informed them it was because favourable lease terms could not be agreed with the landlord.
A spokesperson said: “We have been looking at our options, but the reality is that we have been unable to reach an agreement with the landlord that makes this store commercially viable."
Jerome Saint-Marc, Wilko CEO commented: “Our history is steeped in serving our customers and communities going back to 1930 but there’s no denying the way people shop with us and where they want to shop with us is changing.
"As a business we’re evolving and this includes working with landlords for more favourable terms, as well as looking at locations and store formats.
"We’ll continue to pull together to make our business better to secure the future of over 16,000 team members.
“We’ll be doing everything we can to support our affected team members who will be offered any available positions in nearby stores. We apologise to customers but will continue to offer them everything they need in nearby stores or via wilko.com.”
The announcement comes with a call from the GMB Union for a commercial rents overhaul.
Roger Jenkins, GMB National Officer, said: "These closures are devasting for Wilko workers and the communities who use them.
“It’s yet another nail in the High Street’s coffin and GMB calls on councils and landlords to review commercial leases and offer lower rents.
“Empty high streets and shopping centres are in no one’s interest and but with 400 shops a week closing, this is inevitable - unless the costs of premises can be reduced.
“GMB will now meet with Wilko members to discuss our next steps.”