Flights in and out of the hub were being affected but a company spokesman said the situation was calm and that Lufthansa was confident it would operate all 32 flights it had promised would take off.
In its fourth labor action in recent weeks, the pilots' union Vereinigung Cockpit called on its members to strike on long-haul flights departing from the airport between 8:00 am and 11:00 pm (local time).
Affected were flights operated on Airbus A380, A330 and A340 aircraft, as well as Boeing 747 jets.
Lufthansa's pilots are striking over changes to their retirement benefits being introduced as part of deep restructuring in recent years to bring down the German carrier's costs.
Pilots can currently take paid early retirement from the age of 55. They are fighting a plan by the airline to raise the minimum age and to involve pilots in the financing of their pensions.
Today's work stoppage was the fourth by the pilots' union in recent series of bottom-line-hitting operations.
The first strike at the end of August hit Lufthansa's low-cost subsidiary Germanwings. The second walkout hit from Frankfurt and the third stoppage targeted Munich airport, Germany's second-busiest air hub.
Many of Europe's older airlines are running into opposition from powerful unions as they try to cut costs to compete with budget rivals.
On Sunday, Air France's main pilots' union ended the longest strike in the carrier's history to allow "calmer" talks to go ahead over the contentious issue of the airline's low-cost subsidiary Transavia.
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