Luke Glendenning of Swarcliffe died of multi-organ failure following complications during the surgery at Leeds General Infirmary in November 2017, the inquest at Wakefield heard.
Recording a verdict of misadventure following a two-day inquest, assistant coroner Oliver Longstaff, said: "The surgical procedure that Luke underwent on November 6 (2017) was
undertaken deliberately and undertaken in what was perceived to be Luke's best interests.
"The events that followed from that surgery were unforeseen, unintentional and a tragedy."
The inquest heard Luke was fit and healthy and that the kidney stones were an incidental finding following a fall earlier in 2017.
He suffered complications during the surgery including internal bleeding and a rare condition called abdominal compartment syndrome.
That condition came about after fluid put in his system during the operation failed to drain properly and put pressure on his organs.
The inquest heard he underwent five more operations, but died on November 9.
The inquest heard that the paediatric percutaneous nephrolithotomy operations of the type that Luke underwent are no longer carried out at in Leeds and there are no plans to reintroduce them.
Luke's mother Sue Hirst said after the inquest: "We were never told of the risk of the fluid and that it might lead to abdominal compartment syndrome."
Miss Hirst said there should have been more checks in place during the operation to ensure that the condition was not occurring.
Miss Hirst and Luke's father Richard Glendenning wrote in a joint statement: "We feel the trust completed a thorough investigation and we have had the opportunity to meet with them in order to discuss their findings."
They added: "Luke was described by his friends as 'small boy with a big heart.' He was funny and popular, enjoyed playing out with his friends and also on his Xbox.
"He was our only child and losing him has left a massive hole in our lives.
"Our hope is that lessons have been learned following Luke's death and that the NHS will implement changes so that no other child or family has to go through what we have gone through.
We hope that this will be Luke's legacy."
The inquest heard that there was no reliable monitoring of the fluid that built up in his body during the operation.
Assistant Coroner Oliver Longstaff said the irrigation fluid put into Luke’s system to clear debris did not drain properly and collected in his abdomen, causing it to swell.
But the worsening condition, which resulted in abdominal compartment syndrome, was not noticed because Luke was laid on his front during the operation, which involved puncturing a hole in his kidney to insert a tube and a small camera.
Mr Longfstaff accepted the doctors’ approach on the day of Luke’s death was “common practice”.
The coroner encouraged NHS England to conduct a review to determine whether sufficient measures are in place to monitor fluid output or the condition of a patient’s abdomen during the percutaneous nephrolithotomy surgery.
He said that the surgery is no longer carried out in Leeds due to a “lack of confidence.”
Dr John Adams, associate medical director for risk management at Leeds Teaching Hospitals NHS Trust, told the inquest there are currently no paediatric percutaneous nephrolithotomy operations carried out in Leeds and that there are no plans to reintroduce the operations. He said cases are transferred to hospitals in Sheffield.
Leeds Teaching Hospitals NHS Trust’s chief medical officer Dr Yvette Oade apologised after the inquest.
Dr Oade, said: “I offer our sincere condolences to Luke’s family and say how sorry we are that Luke died whilst he was in our care.
Since Luke’s death we have reviewed this procedure and it is no longer undertaken in Leeds. We are committed to ensuring the lessons we have learned are shared with other trusts so this does not happen to another child.
“We fully accept the findings of the coroner and offer our heartfelt sympathies to Luke’s family.”
Towards the end of the five-hour operation, doctors noticed Luke was unable to maintain his own blood pressure, the inquest heard.
His legs had also gone pale and he had suffered a rectal prolapse and a distended abdomen, which means his stomach was severely swollen, doctors said.
He had contracted abdominal compartment syndrome..
Doctors told Luke's parents they could not remove all the stones because Luke had an abnormally formed kidney.
Scans revealed Luke had fluid on his lungs and in his chest and he underwent further surgery that evening to remove his left kidney.
Luke underwent his third operation in under 24 hours in the early hours of November 7, 2017, this time to try and drain some of the fluid from his body.
Following that operation the youngster's extremities were cold and his skin was starting to turn yellow, according to a statement provided to the court by Miss Hirst.
Doctors were also struggling to find Luke's pulse and he was taken back into theatre to remove packs that had been placed to drain the fluid, but which might have affected his breathing.
Following that operation he was taken into intensive care and placed on a machine that supported his heart and lungs.
However, Luke's heart stopped beating and he underwent a sixth and final operation to try and restart it, after which he was placed on life support.
The inquest was told Luke's life support was switched off on November 9.