Workers at Berlin's Tegel and Schoenefeld airports will walk out at 4 am local time (0300 GMT) on Monday and end the strike on Tuesday at about 5 am local time (0400 GMT), said Verdi in a statement.
Lufthansa said it would cancel all flights on Monday from Frankfurt and Munich to Berlin, and from Germany's capital to those cities. It did not say how many flights that involved.
The union wants an increase in pay for ground staff to 12 euros ($12.80) an hour from about 11 euros as part of a one-year collective agreement. Management first offered about 10 cents more an hour over four years and then improved that offer to an 8 percent increase over three years.
"The volume is too small and the duration far too long to find a compromise on this basis," said Verdi negotiator Enrico Ruemker in a statement.
As well as Lufthansa, carriers including Air Berlin , easyJet and Ryanair serve the two airports.
Groundstaff jobs include checking in passengers, loading and unloading planes and directing aircraft on the tarmac.
Tens of thousands of passengers were stranded in Berlin on Friday as the last strike by ground staff led to the cancellation of nearly 700 flights.
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