Dublin boy Reese Kilbride, 12, wrote a letter after learning about the 1916 Easter Rising at school.
The reply, written by a palace official, said: "This is not a matter in which Her Majesty would intervene."
Reese's mother, Fiona Dowling, said her son had not expected a response.
"I told him not to expect anything given she gets loads of letters," she said.
"They were learning about the Easter Rising in school, it's been a key theme for them this year and Reese was just really interested in it."
Reese asked for "the return of the six counties" and enclosed drawings of himself and his friend, Ethan.
In reply, Jennie Vine, a deputy correspondence co-ordinator at the palace, said: "Her Majesty has asked me to thank you for the pictures you drew especially for her".
On the matter of Northern Ireland, Ms Vine said that "as a constitutional sovereign the Queen acts on the advice of her ministers and remains strictly non-political at all times".
Asked what Reese has done with the letter now, Ms Dowling said: "He took it to school to show his class.
"I was going to frame it, but last night I found it scrunched up in the bottom of his school bag!"
An Irish primary school pupil who wrote to the Queen requesting that she turn Northern Ireland over to the Republic of Ireland has received a reply from Buckingham Palace.