Jonjo Heuerman, from Dartford, has raised more than Â£235,000 for Cancer Research UK's Bobby Moore Fund.
"It was a big surprise, because I never thought I could get something like this at this age," the teenager said.
"It made me feel quite proud of myself because I've worked really hard over the last five years."
He added: "In 2009 my nan died from bowel cancer - she had been fighting it for a very long time.
"My football hero Bobby Moore also died from it about 20 years ago, and I decided to fundraise for the Bobby Moore Fund."
The teenager has walked and cycled thousands of miles across Britain since the death of his grandmother Lyn.
In 2014 he dribbled a football from Southend to West Ham United's ground over five days, covering 50 miles.
Jonjo said the hardest challenge had been in February when he undertook a 700-mile cycle ride, visiting all of the Premier League football clubs in England.
He then returned to London and walked to all of the capital's Premier League clubs.
"I'm in training for the next one which is in April. I'm going to be cycling and walking from Germany all the way to the UK," Jonjo said.
His mother Donna said that after finding out about the award in November, the hardest part had been keeping the news from Jonjo's grandfather Brinsley.
"He and Jon are very close and he was busting a gut to tell him," she said.
Bobby Moore's widow Stephanie praised the teenager's efforts.
"Not only has he raised a phenomenal amount of money and helped raise awareness of bowel cancer, but he has taken on a huge physical challenge for someone so young," she said.
Jonjo said he did not think his friends would believe he had been awarded the British Empire Medal.
"It is really special and it is a motivation for me. I know I've got lots more work to do.
"I want to get another Â£100,000 for another research project I want to fund."
Jonjo is one of nearly 1,200 people who have been named on the New Year Honours list.
Nearly three-quarters of the recipients have been recognised for work in their local communities. However, some of the more famous faces to receive awards include Barbara Windsor who has been made a dame and cyclist Chris Froome who has been appointed OBE.
A prolific schoolboy fundraiser has been awarded a British Empire Medal  - and at the age of 13 is the youngest person on the New Year Honours list.