The award, which the Tottenham striker will receive at a ceremony in January, will be made in recognition of his outstanding sporting achievements.
One of the City of London's ancient traditions, the Freedom is believed to have begun in 1237 and enabled recipients to carry out their trade.
Kane, 29, was nominated for the award by the City of London Corporation's policy chairman Chris Hayward and deputy policy chairman Keith Bottomley.
The award was agreed by the City Corporation's elected Court of Common Council.
Kane said: "I am extremely proud and grateful to be awarded the Freedom of the City of London award. This is a proud moment for myself and my family.
"It is a real honour to be recognised by the city I grew up in and love, and I am looking forward to meeting those who nominated me at the award ceremony."
Hayward said: "We are delighted that Harry will be awarded the Freedom of the City. It is richly deserved.
"Harry is a superstar for so many football fans. He has made a massive contribution to sport and London."
Born in Walthamstow, north London, Kane is a product of Spurs' academy and made his England debut in March 2015 against Lithuania.
As well as being nominated for, or applying for the Freedom, it is also offered by the City of London Corporation to individuals as a way of paying tribute to their outstanding contribution to London or public life, or to celebrate a very significant achievement.
In August, it was announced that the entire England Women's team would be awarded the Freedom of the City of London following their European Championship triumph.