Bite The Ballot and Hope not Hate aim to sign up 500,000 young people to vote by the 7 June registration deadline.
They say interest in the 23 June poll is high although the campaign is perceived as being dominated by "old men shouting at each other".
Young people are twice as likely not to be signed up as the public at large.
In five weeks' time, the UK will decide whether it should remain a member of the European Union or not, with British citizens aged 18 and over and specified others entitled to vote. It will be the first public vote on the country's future in Europe for more than 50 years.
Amid concerns about levels of youth turnout, efforts are being stepped up to encourage young people to sign up to vote in time to take part. Those who registered ahead of the local and national elections on 5 May do not need to re-register.
The #TurnUp campaign, which launches on 31 May, is focused on getting young voters to encourage their friends and colleagues to sign up at events in universities, youth clubs, workplaces and cafes.
A survey of 1,300 18-30 year olds carried out by YouGov suggests 51% are closely following the referendum, 39% are not while 10% are avoiding coverage of it altogether.
While the majority - 52% - of those polled said the economy was the most important issue in determining how to vote, the research found low levels of trust in those representing either side in the referendum debate.
Only 10% of those canvassed trusted politicians to make the case for either a Remain or Leave vote, while the figures for the media (13%) and business leaders (16%) were only slightly higher. In contrast, teachers and academics scored much higher levels of trust (72%) as did other young people (50%).
Bite the Ballot's director Mike Sani said it was vital the campaign was not merely the preserve of politicians and business people.
"We need to act now to ensure those unregistered are empowered and inspired to take a role in the decision-making process," he said.
"Young people will be living longest with the outcome and the risk of not engaging them in the issue is too big to ignore."
And Hope not Hate said there would be serious consequences if young people were shut out of the debate.
"It is vital they get registered but also vital for both Remain and Leave campaigners to address the concerns of the young far more directly," said its chief executive Nick Lowles.
"We know that if they don't, and the voices of the young are not heard, disaffection can breed alienation. That in turn can act as a potent lure for extremists and others who would divide society."
The groups say 30% of all 18-24 year olds are not registered to vote at the moment and, of those who signed up to vote in last year's general election, only 54% ended up voting - much lower than other age groups.

2 December 2015 Last updated at 09:17 GMT
Emi, 22, wrote The Things She Told Me to reflect her own experiences as a woman, but she hopes it will resonate across the world.
The Sudanese-American who originates from Darfur only began writing slam poetry - work that is written for performance and that is often powerful and emotional in tone - when she arrived at university.
She is studying anthropology and molecular biology at Yale, and is one of the BBC's 100 Women 2015
Our 100 Women season showcases two weeks of inspirational stories about the BBC 100 Women and others who defy stereotypes around the world.
Like us on Facebook, follow us on Instagram using the hashtag #100Women and listen to our programmes here.
Young people must be "inspired not ignored" in the EU referendum debate, campaigners said as they began a drive to boost turnout among 18-24 year olds.
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Emi Mahmoud, the reigning World Poetry Slam Champion, has written a poem for the BBC 100 Women season.