The sapling, one of a special type, was located on the grassed area next to the River Leen.
But a spokeswoman for Nottingham City Council parks department said the tree had evidently been dug up and stolen.
The tree planting was a highlight of a memorable Jubilee event at the Bogs on June 2, which was climaxed by the lighting of beacon.
UPDATE: Missing Hucknall man Owen Goodman has been found
Hucknall: Police investigation underway after attempt to break into town B&M store
Hucknall lady Mavis enjoys fizz and style as she turns 100
Hucknall residents demand answers why bid to boost town is £11m and not £20m - council explains
Hucknall man prosecuted and fined £1,000 for failing to remove rubbish from garden
The vicar at St Mary's Church in Bulwell, Father Andrew Fisher, performed the planting after winning the privilege of doing so as the result of a raffle.
When told of the theft, he said: "You would not credit it that something like this could have happened."
Former Dispatch chief reporter Denis Robinson had been keeping an eye on the tree during regular visits to the Bogs with his four-year-old great-niece, Isabelle Gee, who likes to play on the 'pirate park'.
Denis said: "I could hardly believe it when I found that the tree was not there any more.
"It is probably now in somebody's garden."
The Parks Department spokeswoman said it was planned to provide a cherry tree as a replacement in the early autumn.
A spokesman for the Friends of Bulwell Bogs group, which hosted the Jubilee event, described the loss of the apple tree as 'very disappointing'.
As the Dispatch exclusively reported, a controversial plan for large-scale changes to the Bogs, including two new bridges over the Leen, was scrapped after strong opposition from the Friends group.