The Tottenham striker and England captain is receiving the honour in recognition of his 'outstanding sporting achievements'.
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The 29-year-old, who has - loans aside - spent his entire professional career at Tottenham, will receive the award at a ceremony in January when he arrives back from the World Cup in Qatar.
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 was nominated for the award by the City of London Corporation's policy chairman Chris Hayward and deputy policy chairman Keith Bottomley.
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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."
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Mr 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."
Kane has played 75 times for England and scored 51 goals, and is closing in on Wayne Rooney's all-time record of 53. He was the top goalscorer at the 2018 World Cup to win the Golden Boot.
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Despite not winning any major trophies, Kane is the third-highest goalscorer in Premier League history with 193 goals and boasts three top flight Golden Boots awards
The annoucement comes the day after Jurgen Klopp was awarded Freedom of the City of Liverpool.
The Reds manager vowed to defend Liverpool 'forever' as he was honoured in a ceremony held in the city's Town Hall on Wednesday evening.
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Although the German admitted he was left confused by one of the laws of the historic award, which gives the holder the right to drive sheep through the city streets.
Unbaalievable!