According to the Daily Mail newspaper, a number of organisations, including Amazon and Microsoft, appeared alongside videos that promoted eating disorders and self-harm.
The newspaper said that a CAF advertisement had appeared alongside one of the videos, which was apparently promoting anorexia as a positive lifestyle choice.
Google adverts are normally placed by automated technology, and an advertisement appearing alongside a YouTube video earns whoever posts the clip a share of any advertising revenue.
A CAF spokesman said: "We have been actively screening our advertising to ensure that adverts are not placed alongside inappropriate content.
"Once this advert was brought to our attention, we removed all of our YouTube advertising until we can be reassured that nothing like this will happen in future."
In a blog post on the CAF website, Adam Pickering, international policy manager at CAF, said the charity would now place advertisements on "a select few websites" where CAF had "confidence in the nature of the content our name will appear next to".
According to an investigation by The Times newspaper in February, a number of other organisations, including charities, have unwittingly advertised alongside YouTube videos that promote extremist content. These have included content from Nazi groups and Islamic State.
In February, Marie Curie withheld a "significant proportion" of its digital advertising activity, including all of its YouTube adverts, after one of its adverts appeared alongside a video posted by the pro-Nazi group Combat 18, according to The Times.
YouTube’s harmful or dangerous content policies prohibit videos that promote dangerous or harmful activities, but their removal is reliant on viewers flagging videos to YouTube.
A spokeswoman for YouTube said: "Videos that encourage people to commit harmful or dangerous acts are against our policies and we remove them when flagged.
"We also know that many people come to YouTube for emotional support and continually try to strike the right balance to enable people to talk honestly about the issues they’ve faced and provide support. We are, however, careful to age-restrict material that might not be suitable for younger users."
Google has also expanded safeguards for advertisers and has made a public commitment to give advertisers more control over where their advertisements appear.