Activities have included an annual five-a-side football tournament where 500 pub teams took part and raised more than £400,000.
Hundreds of thousands of pounds were raised by customers and staff participating in a range of events such as quizzes, raffles, challenges and runs.
JD Wetherspoon CEO Tim Martin said: “We are immensely proud of the partnership that we have with CLIC Sargent.
“When it started we had no idea how much we would raise.
“Now we know that our hard-working and committed staff and customers will have made a real difference for so many families struck by cancer.
“The £13m total is fantastic but we know that the fight for young lives is ongoing and we want to help CLIC Sargent be there for young cancer patients and their families in the future.”
A battle you don’t feel like fighting
JD Wetherspoon representatives were thanked by two teenagers, who were supported by the charity.
One of the teenagers, Tyler Hart, is coming to the end of an intensive course of chemotherapy after being diagnosed with blood cancer non-hodgkin lymphoma
His mother Sue said: “I met a CLIC Sargent social worker Jan Roberts and she offered us a grant of £170 which was a massive help with our debts piling up.
“We got on really well and if I had any worries I could text or phone her.
“When I was struggling, I could just talk to her easily and it really helped.”
The family of the other teenager, Tilly Somervell, stayed at Paul’s House, CLIC Sargent’s Home from Home in London during her treatment for thyroid cancer, which helped them avoid a regular three-hour round trip.
Her mother Jo said CLIC Sargent felt like another line of defence as fighting cancer is a battle that she sometimes didn’t feel like fighting.
“I don’t have to do it alone”
She added: “Without CLIC Sargent it would have been very lonely. With their support, I don’t have to be a one-woman fighter, I don’t have to do it alone.”
CLIC Sargent corporate events executive Jemma Syms said the £13m was a testament to the commitment and hard work of the pub chain’s staff.
She added: “It is an incredible total and will help CLIC Sargent fight for young lives against cancer.
“When a family hears the doctor say ‘it’s cancer’, life can stop.
“From that point, CLIC Sargent is there, providing vital, frontline services like social workers and financial grants, to help families limit the damage cancer causes beyond their health.
“The partnership between JD Wetherspoon and CLIC Sargent is the longest-running in the charity’s history and we have been blown away by the ongoing dedication and enthusiasm shown by JD Wetherspoon staff to help CLIC Sargent fight for young lives struck by cancer.”