Lyttelton Port of Christchurch sustained several million dollars worth of wharf and infrastructure damage in the quakes, which happened in September and February, but it was able to resume operations relatively quickly on both occasions.
Lyttelton's township was near the epicentre of the quakes, and many older buildings were destroyed.
Port Otago commercial manager Peter Brown said many of Port Otago's 300 staff donated a day's leave, the value of which was matched dollar-for-dollar by Port Otago and topped up to the final $50,000 figure.
"It's a matter of one port town wanting to do something for the community of another port town," Mr Brown said.
Port Otago chief executive Geoff Plunket was scheduled to present the donation to the Lyttelton Harbour Rotary, at Naval Point Yacht Club, last night. The funds would go toward the support of youths and the elderly in the harbour area.
