A professor who was ordered to stop using what his patients called “life-saving” treatments has been allowed to reopen his clinic – after the parents of a six-year-old girl took hospital chiefs to the High Court.

Dozens of Professor James Malone-Lee’s patients arrived at the Royal Courts of Justice this morning to hear whether health bosses at Whittington Health NHS Trust acted unlawfully when a clinic treating recurring urinary tract infections (UTIs) was suspended last month due to safety fears.

More than 900 people from all over the UK came to receive Prof Malone-Lee’s “unorthodox” treatment at his clinic in Crouch End, with his use of high dose antibiotics heralded by patients as “life-saving” and “the only treatment that works”.

The clinic was closed, however, after Prof Malone-Lee was ordered by Whittington Health to only administer care according to NHS guidelines. This involves short term courses of antibiotics – described by many patients with recurring infections as “useless”.

The Whittington’s medical director, Dr Richard Jennings, said the decision – which he described as a “judgement call” – followed a “safety alert” after a patient suffered serious organ damage thought to be caused by an antibiotic that was prescribed “at a higher dose than is recommended, for a much longer duration than is recommended”. This was said to mirror an incident six years ago.

But the closure prompted a furious backlash from patients who said it would mean a return to lives blighted by chronic pain.

Almost 5,000 people signed a petition calling for the clinic to be reopened, with patients saying they were made aware of any risks. They warned medical chiefs at Whittington Health that people would be left suicidal if the clinic was not reopened.

Today, lawyers acting on behalf of a six-year-old patient of Prof Malone-Lee’s argued in the High Court the decision by the Trust to close the clinic without involving patients in the decision making process was “unlawful”.

The mother said in a statement before the case: “My six-year-old daughter was treated by other clinicians, but continued to deteriorate. She was then referred to the LUTS clinic under the care of Professor Malone-Lee. By the time she reached the Professor’s clinic she couldn’t sleep at night, and had problems attending school.

“The Professor’s treatment turned her life around so she could live again.

“She was able to enjoy life, like any other normal healthy child. The school was amazed at the difference, and her attendance has improved along with her ability to concentrate and learn. She is still undergoing treatment with the Professor and we were devastated to hear of the closure of the clinic.

“No one is now monitoring my daughter’s treatment or care, despite desperate attempts to contact the Whittington for help. The Professor was a tertiary consultant, and there is no other clinician in the country to replace him.

“I am desperately worried for my daughter’s future now that the clinic is closed. She had very little quality of life before treatment, and I worry that she will go back to debilitating pain now that the clinic is closed.”

It emerged during today’s court hearing the trust had come to an agreement with Prof Malone-Lee yesterday, allowing him to reopen the clinic with “certain restrictions”.

Patients at the High Court, many of whom had confronted Whittington board members during the monthly board meeting earlier this month, cautiously welcomed the result.

A spokesman from Whittington Health said: “At a hearing today, the Court approved an arrangement agreed between the Trust and the representatives acting for the Claimant.

“In advance of the case today, we agreed with Professor Malone-Lee a new framework for treating patients at the Lower Urinary Tract Service (LUTS) and are working to reinstate the clinic as soon as possible.

“Following an alert about a safety incident, and in order to protect patient safety the outpatient clinic that was being held at Hornsey Central Neighbourhood Health Centre was suspended. The clinic provided the LUTS.

“This change was necessary because of concerns about possible risks to the health of patients associated with some of the antibiotic prescriptions and potential long-term severe organ damage.

“We recognise that this has been a particularly difficult time for patients and their families and would like to apologise for any distress this suspension has caused.

“We would like to reassure patients and their families that delivering good, safe care remains our first priority and we will continue to work closely with Professor Malone-Lee to deliver the service.”