The fund was set up in the memory of Faversham schoolboy Silas Pullen, who lost his brave battle with an aggressive form of brain cancer in 2013, at the age of 11.
The Sheps Giving committee will be working with The Silas Pullen Fund and The Brain Tumour Charity to organise fundraising activities at the brewery and across its pub estate throughout the next 12 months.
Chief executive Jonathan Neame said: "We are committed to supporting the community we serve, and are delighted to announce this partnership with such a worthy cause.
"The Silas Pullen Fund has special significance for our company, not only because of the Pullen family's local links, but because we have lost two members of staff to the illness, and several other employees have lost loved ones.
"By choosing the Silas Pullen Fund as our Charity of the Year, we hope to not only raise a significant amount of money, but also raise awareness of this devastating disease."
Silas' Mum Sarah Pullen said: "My husband Ben and I are delighted that Shepherd Neame have chosen the Silas Pullen Fund as their Charity of the Year. It is fantastic to be supported by a national business with such strong local connections.
"We look forward to working with their team to raise awareness and funds and make a real difference to other families affected by a brain tumour."