The money was raised in support of CLIC Sargent, a support charity which fights for young lives struck by cancer.
The milestone means fundraisers in J D Wetherspoon pubs across the UK are now raising as much as £1.6 million every year. The most recent million was raised in just seven months.
Representatives of J D Wetherspoon were thanked by two teenagers who are supported by the charity, Tyler Hart and Tilly Somervell.
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 her or phone her. When I was struggling I could just talk to her easily and it really helped."
Her mother Jo said: "CLIC Sargent feels like another line of defence - it's all a battle and sometimes you don't feel like fighting. Without CLIC Sargent it would've been very lonely. With their support I don't have to be a one woman fighter, I don't have to do it alone."
Major recent events include an annual Kick five-a-side football tournament, in which more than 500 pub teams took part and raised more than £400,000. Hundreds of thousands of pounds were raised by staff and customers taking part in a variety of events including quizzes, runs, raffles and challenges.
The bumper total was just a speck on the horizon when the partnership was formed 14 years ago when pub chain founder Tim Martin fortuitously found himself sat opposite the then chief executive of the charity on a train. The pair struck up a conversation and were inspired to launch a partnership, with an initial target of £500,000. The partnership continued to blossom, with staff beating targets year on year.
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 £13million 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."
Jemma Syms, CLIC Sargent Corporate Events Executive, said: “This £13 million fundraising achievement is testament to the commitment and hard work of the J D Wetherspoon staff. 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 J D 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 J D Wetherspoon staff to help CLIC Sargent fight for young lives struck by cancer.”
CLIC Sargent supports families through a variety of services including social workers, nurses, key workers, play specialists and financial grants. For more information visit www.clicsargent.org.uk