Her Lumos Foundation is raising money to provide food and hygiene and medical kits to those affected by the conflict, as well as helping to support their evacuation from the country.
Money raised will also go to providing psychological support to children impacted by the conflict, and supporting families and foster carers.
The Harry Potter author, 56, tweeted: “War shatters childhoods and tears families apart.
“@lumos has launched an appeal to help the c100k children trapped in orphanages in #Ukraine.”
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The charity has been working with the Ukrainian government to reform its care system and better protect vulnerable children.
A message on its website warned the Russian invasion “means more children are now in danger”.
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Lumos, which was co-founded by Rowling in 2005, has been operating in the Zhytomyr region, which lies to the west of the capital of Kyiv.
It estimates there are more than 1,500 children trapped in orphanages there, with thousands more at risk of displacement and family separation.
A Russian military convoy around 40 miles long is north of the Ukrainian capital and there are fears that the city will face a barrage of rockets and shells.
Ukraine has accused Russia of war crimes over the bombardment of civilian areas in the second city Kharkiv.
It has also been claimed that Russian forces have deployed thermobaric rokets. The so-called ‘vacuum bomb’, which Ukraine says the Russians have used in the invasion, ignites a fireball that sucks in all surrounding oxygen