The 73-year-old Welsh star will be honoured for his career spanning some five decades at a London ceremony on 4 July.
Organisers described Sir Tom as "a living legend" whose music had "brought pleasure to many people".
The Silver Clef Awards raise funds for the charity Nordoff Robbins to provide music therapy for adults and children.
"To be presented with the lifetime achievement award is a great honour," Sir Tom said.
"I've seen first hand the amazing results that the dedicated and skilful therapists get with children and adults - it's work that really makes a difference.
"This is a wonderful and important charity, so to be recognised for my lifetime of work means a great deal."
The singer first rose to fame as a solo singer in the 1960s with hits including It's Not Unusual, What's New Pussycat? Green, Green Grass of Home and Delilah.
He went on to sell more than 100 million records around the world, scoring 46 top 40 singles in the UK and 19 in the US.
Other award recipients revealed on Tuesday included Laura Mvula, who will receive the best newcomer prize, and pop duo Chas and Dave who will be presented with the Icon award.
They join previously announced winners Pharrell Williams (international award), Paloma Faith (best British act), Gareth Malone (Classical award) and Italian producer Giorgio Moroder (Innovation award).