I have seen at least two sources that have said that children were guillotined during the French Revolution.

Thomas Carlyle wrote a history in the 1830s that was entitled The French Revolution: A History.  He says at least twice in that book that children were executed by the guillotine.  However, this was a different era in historical writing and he gives no numbers (if, indeed, any could possibly have been available).  He says of a Representative Lebon from Arras:

Mothers, they say, by his order, have to stand by while the Guillotine devours their children...

At the beginning of Chapter 3.5.III he says

Little children are guillotined, and aged men.

Carlyle's book is well respected, and he does cite sources for these claims.  However, there are no numbers given.

A source that does cite numbers is Barbara Levy's Legacy of Death.  I do not have the book with me any more, but I have in notes that I have used for teaching that she says more than 20 people under 18 were guillotined in Paris during the Revolution.  Would these be considered children? It is not clear because I do not think she gave ages.

So, it would appear from sources that some children were guillotined.  But it is not clear how many or of what ages.