Mayor Celia Wade-Brown said the award was a fitting recognition of McCullum's achievement.
"Wellingtonians and the cricket world congratulate Brendon McCullum on his magnificent achievement," she said.
"The Basin Reserve is rightly regarded worldwide as a special Test venue and has hosted many triumphs and dramatic moments.
"Brendon's magnificent innings will be remembered for decades to come by the thousands of people at the Basin, and the tens of thousands of others who stopped everything in the middle of a working day to witness sports history being made."
She said the honour will ensure McCullum, who lives in Christchurch, will always be "at home" in the city of his greatest sporting performance.
McCullum said he was "honoured and humbled by the gesture".
He indicated he will accept the keys a ceremony, expected to be in June.
After helping win the 2005 Ashes series, English talisman Andrew `Freddie' Flintoff was awarded the freedom of his home city of Preston.
It was said that the honour gave him the ancient privilege of being allowed to herd flocks of sheep through the town.