He will join recent departee Kate Daughton, formerly his Head of Comedy Commissioning, to launch a new production company "specialising in scripted comedy and comedy drama".
Allen has been in the BBC role - previously known as Controller of Comedy Commissioning - since 2012, and held the equivalent post at Channel 4 before that. The BBC will begin recruitment immediately for a new Director of Comedy, ahead of Allen's departure in August.
Shane Allen says: "I've felt like a competition winner every single day working with the cream of creative talents at the broadcaster which is so synonymous with the story of British comedy. Now feels an opportune time to start a new career chapter as the world opens up again and British comedy talents continue to take the world by storm."
Allen and Daughton are founding the new company together and will both use the title Chief Creative Officer.
The BBC says: "Shane Allen is a passionate supporter of new talent and has been instrumental in launching a range of new initiatives from BBC One's Comedy Playhouses, BBC Two's New On Two strand and Comedy Slices and Threesomes on BBC Three, which continues to be a vital place to develop the next generation of on and off-screen comedy talent.
"His iPlayer comedy shorts strand uniquely offered generation defining comedy talent the space to experiment with ideas, concepts and formats many of which have gone onto series with Gbemisola Ikumelo's Brain In Gear winning the BAFTA Short-form category most recently. Foot in the door opportunities he launched include The Felix Dexter Bursary to open opportunities for diverse talent, The Galton & Simpson Bursary geared towards mental health support, and The Caroline Aherne Bursary whose inaugural winner Sophie Wilan is one of the BAFTA nominees this year with Alma's Not Normal."
The continue: "In 2021, Allen established the BBC Comedy Association to engage and enable a new wave of talent on and off screen including the return to television of the New Comedy Awards to ensure that BBC comedy is at the forefront of supporting the industry across the UK at all levels in 2021/22 and beyond. During his tenure as part of this initiative BBC comedy has partnered with multiple productions to bring through trainees from under-represented backgrounds off screen in a variety of roles.
"Most recently, Allen masterminded the Festival Of Funny - a pan-BBC celebration of British comedy to put a smile on faces across the country through the pandemic. Last week it was announced that BBC Three is the first broadcaster whose scripted comedy output has a majority female leaning in authorship for scripted comedy the year ahead."
Lookout Point explain: "The duo plan to create a range of high-profile shows which capitalise on the rising global appeal of British comedy, with the potential to work across the full spectrum of channels, platforms and audiences, and harnessing their excellent relationships with A list talent and media outlets around the world."
Its CEO, Faith Penhale adds: "Shane and Kate really are the best in the business. As their truly spectacular list of credits proves, they have an unerring eye for the most brilliant, original talent and they know how to turn great ideas into era-defining, world-conquering shows. It is a privilege to be joining forces with them as they take this exciting next step together."
Charlotte Moore, BBC's Chief Content Officer, says: "Shane is an extraordinary creative whose passion for spotting exciting new talent and pushing comedy boundaries has had a remarkable impact on the whole British comedy industry for the best part of a decade. From Fleabag to Car Share, This Country to People Just Do Nothing, Inside No. 9, and Motherland to Famalam, the range, the quality and the sheer ambition of BBC comedy has kept audiences laughing year in year out.
"And his pioneering work to support new talent has led to a golden age for British comedy, winning more awards, launching more new voices on the global stage and commissioning more hits than any other broadcaster. He leaves BBC comedy in rude health but we owe Shane a great debt of gratitude and I won't be alone in saying I will miss him greatly both personally and professionally."
Kate Phillips, Director of BBC Entertainment, will now oversee new scripted comedy commissioning decisions whilst Allen oversees ongoing productions and works on the BBC Comedy Association's inaugural year plans for a city of comedy, appointment of a Young People's Comedy Laureate and the TV re-boot of The New Comedy Awards.