According to the airline’s website, 16 flights between Stockholm’s Arlanda airport are affected along with eight flights out of Gothenburg’s Landvetter airport.
Flights to Munich from both airports are unaffected because routes to Sweden from the southern German city are managed by Lufthansa’s subsidiary Eurowings, which is not participating in the strike.
The airline said on Thursday that 50 percent of flights on Friday would be affected, affecting 84,00 passengers, after German pilots’ union Vereinigung Cockpit announced its staff would continue to stay away from work.
In addition, a planned strike by air traffic controllers in Italy – completely separate from the pilots' strike — may result in the cancellation of a further 90 flights affecting 10,000 passengers, Lufthansa said.
Lufthansa said its long-haul services should not be affected and will take off as scheduled.
"All flights by Germanwings, Eurowings and Air Dolomiti, as well as Swiss, Austrian Airlines and Brussels Airlines will go ahead as planned," the carrier said.
The pilots' union Cockpit had initially called for 24-hour walkout on Wednesday, but subsequently extended the industrial action, first to Thursday and then to Friday.
On Wednesday, the stoppages had targeted short- and medium-haul services.
But long-haul flights were grounded on Thursday, affecting 18,000 passengers.
Cockpit has staged more than a dozen sets of strike action since last April over management plans to change the pilots' early retirement arrangements.
The dispute hinges on plans by Lufthansa to scrap an arrangement under which pilots can retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Pilots are also concerned about Lufthansa's aim to further develop its low-cost activities as it faces growing competition.
The Lufthansa follows several other strikes by European flights in recent weeks, which have had a particularly bad impact on Scandinavian passengers.