She was believed to have been heading toward the Syrian border settlement of Mayadin as the ISIS capital is besieged by coalition forces.
According to the report, the CIA told the Government in June that the 50-year-old had been killed by a Predator drone that same month.
They did not inform the wider public, however, because there were fears her son Jojo, who is 12, had died in the blast too.
Sources told the paper the strike would have been abandoned if it was known that the boy would be killed.
It remains unclear if he survived the hit.
It was previously reported the terror recruiter was desperate to return home from Raqqa.
Jones was a high priority on the Pentagon's "kill list" because she was believed to have masterminded dozens of terror plots.
The Muslim convert fled Britain to join ISIS back in 2013 alongside toyboy lover and jihadi hacker Junaid Hussain, taking her then-nine-year-old son JoJo with her.
The 12-year-old boy - now named Hamza - is believed to have been forced to execute prisoners during his time there after being brainwashed by violent theocrats.
Hussain was killed in 2015 aged 21 in a US drone strike.
After her husband's death, it was thought she received a monthly salary from ISIS of £520, plus a bonus of more than £200 every couple of months for being the widow of a 'shahid' or martyr.
It was previously claimed Jones was using JoJo as a human shield in an attempt to stop the US from carrying out a similar strike on her.
Last year JoJo's father said his son appeared in an ISIS video showing young boys murdering men in orange jumpsuits.
The man, who asked not to be named to protect his safety, said: "He was brilliant, just a normal boy - always chasing bugs, going down the park. I have had to block it out. It's been hard, we just have to carry on. It's disgusting he's been brainwashed."
Whilst in Raqqa, JoJo was believed to have been brainwashed by IS and taught lessons in martial arts training, firearms and radical Islam.
His name was changed to Hamza and he was forced to call Hussain - his mother's boyfriend - 'dad'.
The boy, also known as Joe, had apparently confided in his grandmother his fear that his mother was planning to take him out of the country.
"He was having difficulty sleeping," said a family friend last year.
"The grandmother discovered that the thing that was worrying him was that his mother was planning a trip."
When challenged, Jones insisted he had made a mistake and that they were merely going on holiday to Turkey.
Friends and relatives, including his grandmother also spoke of their utter grief at being separated from Joe when he vanished with Jones and the trauma of discovering what he was coerced - or at the very least, brainwashed - into doing.
They told how the little boy once called them from Syria, but was prevented from speaking freely by his mother who stood beside him.
They spoke under condition of anonymity for fear, not only of what Jones and her ISIS cohorts might do to them, but of reprisals closer to home from extreme right-wing nationalists.
"I felt sick to the stomach," his grandmother told a friend after seeing the barbaric images of her grinning grandson moments before he shot the prisoner in the back of the head.
"If there is a God, why can't he stop it?" she added.
Relatives described JoJo as a happy little boy who loved reading encyclopaedias and adored animals so much that "he'd never even tread on an ant".
"It's worse than being in mourning," said the family friend who spoke to the Mail.
"They love Joe and miss him but are scared of the forces that have turned him. His grandmother has lost her grandson.
"She doesn't think she can do anything to get him back, and even if he does come back he's not the same boy who went out there."
Major General Chip Chapman, the former MoD head of counter terror, said Jones would have been a "significant" target as a result of her alliance with Hussain and her role in recruiting IS fighters.
Referring to reports her son was killed in the strike, he added: "It is a difficult one because under the UN Charters he is under the age of what we would classify as a soldier."
He continued: "Even if he got up to really bad things, he shouldn't have been targeted.
'We don't know for sure whether he was with her or not."
Jones's supposed desire to return to the UK was revealed by 'Aisha', the wife of another ISIS fighter.
Aisha said she was friends with a British woman called Umma Hussain al Britani - Jones's adopted name - who wanted to return home but was being prevented from leaving by the terrorists.
Aisha said: "She was crying and wants to get back to Britain but ISIS is preventing her because she is now a military wife. She told me she wished to go to her country."
She met Birmingham-based Hussain, who was once jailed for hacking Tony Blair's address book, online where she would reportedly discuss conspiracy theories and black magic in forums.
A prolific social media user, she has used various Twitter accounts to issue terror threats against Britain.
In May 2016 an account claiming to be Jones posted: "To be honest I wouldn't go into Central London through June. Or even July. Well to be honest I wouldn't go there at all, especially by Tube."
According to the Counter-Extremism Project, Jones issued terror threats against Britain as recently as May 2016.
She has previously called on Muslim women to launch attacks during Ramadan in London, Glasgow and Wales.
The group also explains that Jones was a leader of the Anwar al-Awlaki battalion's female wing.
The CEP explains: "In this role, Jones is responsible for training all European female recruits, or 'muhajirat,' in the use of weapons and tactics.
"These muhajirat are then trained and instructed to carry out suicide missions in the West, according to leaked ISIS documents."
She used her Twitter account to express her wish to behead Western prisoners and Christians with a 'blunt knife' and once published a list of 100 US soldiers and their personal information in an attempt to have them murdered by fanatics.
Jones even threatened one of the Navy SEALs who helped kill Osama bin Laden.
It is believed that Jones lived on benefits in Chatham, Kent before converting to Islam.
She had previously worked as a L'Oreal saleswoman.
