The worst-affected airports are Cologne and Stuttgart, but Düsseldorf, Berlin, Hanover, Hamburg and Dortmund have all seen flights cancelled.
Eight flights to and from Vienna Schwechat were also cancelled.
The strike ended on time despite a spokesman for the pilots' union raising the possibility of the action continuing into the weekend.
Aircraft out of position and delays could mean that the airline will cancel further flights in the afternoon.
On Thursday, talks between Lufthansa and the pilots' union Vereinigung Cockpit failed. The two parties could not agree on pension issues for 5,400 pilots.
This is not the first time that Lufthansa pilots have gone on strike over the disagreement. In April, 3,800 flights were cancelled over three days in the biggest strike in the history of Lufthansa. 425,000 passengers were affected.