Its author said he was contacted by Northampton Museum and Art Gallery as it feared the book “had the potential to bring [it] into disrepute”.
Tony Boullemier said he was “delighted” his children’s book was back again.
West Northamptonshire Council runs the museum and said it was removed for the “period of national mourning”.
The Little Book of Monarchs was published in 2013 and charts the history of the Royal Family from 1066.
Its front cover shows a caricature by illustrator Adrian Teal of the then Prince of Wales sneaking behind his mother’s back to grab her crown, while the Queen’s speech bubble says: “Wait for it!”.
Author and local historian Mr Boullemier, 76, who lives in Boughton, near Northampton, said he was surprised the book had been removed from sale – but while he thought it was unlikely to upset anyone, he appreciated the museum’s position.
“I didn’t think it was going to be off permanently because that would have been rather like burning it – which is what they used to do, in fact, they still do in parts of the world,” he said.
“I said I thought it was an over-reaction, but I understand the thinking behind it and so be it, but you will lose some sales.
“On the same day I had another local bookshop that phoned me and said, ‘Can we have another supply, as we’re selling out fast because of the Queen’s funeral?’.”
Mr Boullemier, a former chief sub-editor at the Daily Express who helped to launch the Northants Post in the 1970s before selling the group of 11 weekly papers, described himself as a “history buff”.
“I’m on a mission to improve teaching of history to children – they don’t get a proper run-through of history as we used to,” he said.
“I would say Queen Elizabeth II has not put a foot wrong unlike so many of her predecessors. She is definitely the best.”
Conservative councillor Adam Brown, responsible for housing, culture and leisure, said: “The Little Book of Monarchs was removed by a member of shop staff immediately after the death of Queen Elizabeth II, given the front cover depiction of the new King stealing the crown from behind Queen Elizabeth’s back.
“Museum management agreed it could cause offence to visitors and that it should be removed for the period of national mourning for a beloved Queen, but it is now back on the shelves.”