Equi=Media claims the new campaign marks the first time the has agreed to run full-page ads on its site.
The deal was orchestrated through a partnership with media-buying agency John Ayling & Associates with creative led by Barnardo's agency, BBH.
Barnardo's is launching the online ads to coincide with a wave of television advertising breaking on Monday November 24 on ITV during reality TV programme 'I'm a Celebrity Get Me Out Of Here', and also on Channel 4 and Five.
Online work will appear simultaneously on the Guardian's society and education web pages, and for November 25 Barnardo's has bought home-page takeover placements during key traffic periods.
The campaign aims to raise awareness for Barnardo's following the launch of its 'Believe in Children' strapline last year.
The digital executions build on the TV campaign and highlight the message that behind every troubled child, there are issues which need to be tackled, while demonstrating the charity's valuable work in helping children and young people.
James Miles, digital strategist at Equi=Media, said: "Convincing the Guardian to carry its first full-screen, HD ads is a major coup for us and also for Barnardo's.
"As an agency we are firmly focused on pushing the boundaries of digital to expand the medium into new areas, and this highly impactful ad format should ensure a high-profile online launch, as well as encourage users to engage with the charity."
Barnardo's has recently come under fire for its which shows actors calling children "parasites" and "vermin", culminating with a final scene showing a group of men firing high-powered rifles at a number of children.
The video was to promote awareness of its new study, which found that 49% of adults think children pose an increasing danger to society and 54% say young people are "beginning to behave like animals".
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