Health bosses at an NHS trust thought to be one of only three still providing homeopathy in England are to stop funding the treatment.
Wirral Clinical Commissioning Group (CCG) said 95% of people it consulted wanted to end the £16,500 it spent a year on homeopathy.
However, a homeopathic doctor said it was "a sustainable ongoing" treatment.
Homeopathy uses highly diluted substances that practitioners say can cause the body to heal itself.
'Waste of money'
Dr Sue Wells, Wirral CCG's medical director, said the decision "wasn't about finance".
She said: "We nevertheless need to make sure the considerable money spent is used in the right way and gives the most benefit to Wirral residents."
The National Institute of Health and Care Excellence advises the NHS on the use of treatments and does not recommend homeopathy to treat any health conditions.
Bristol and London are believed to be the only areas left paying for homeopathy, according to the Good Thinking Society, which is campaigning to have it blacklisted on the NHS.
Michael Marshall from the charity said it was "a waste of money" and it was better to allocate resources to treatments with "tangible and clear, proven benefits".
But Dr Adrian Finter, a GP and homeopathic doctor, said he was disappointed.
"If patients are getting themselves better they will be less dependent on the doctor, on the system and the NHS."
Patient Ann Lewis, who suffered from crippling headaches, refused surgery and orthodox treatments in favour of homeopathy.
"I used to have massive headaches - three a week - some of which involved me having to lie in a room with a box over my head because I couldn't stand any light," said Ms Lewis.
"[Homeopathy] stopped them."
About 8,894 homeopathic items were prescribed across England in 2015, NHS Digital data shows.