It says hundreds of doctors, nurses and support staff have died in war zones and when fighting disease outbreaks, such as Ebola, so far this year.
The UN agency says member states and all sides in conflicts must protect health workers and health systems.
It is against international law to target health workers and centres.
According to reports collated by the WHO, the highest number of attacks in 2014 were in Syria, followed by Iraq, Pakistan and Ukraine.
Dr Natalie Roberts, from Wrexham in North Wales, has been working for the past two months with Medecins Sans Frontieres in Yemen, where five health workers were killed and 14 injured in June.
She spoke to the BBC whilst taking shelter during an air raid in the northern city of Saada and said: "Here in Yemen I am supporting five health facilities and three of them have been damaged very badly by bombing, so it does concern me there's a high possibility these places are targeted."
Dr Roberts has worked for MSF in countries including Syria, Ukraine and Pakistan over the last three-and-a-half years and said one of the biggest challenges of working in conflict zones was moving around.
"Even if we mark the cars very clearly with MSF, you can't predict if you're going to pass a checkpoint or market that gets bombed."
Getting caught up in attacks is an occupational hazard for medics working in conflict zones, but the WHO said attacks targeting health workers and facilities was a major concern.
In 2014, WHO says there were recorded (but unverified) reports of 372 attacks on health workers in 32 countries.
These resulted in 603 deaths and 958 injuries, it said.
WHO director-general Dr Margaret Chan said: "Attacks against health care workers and facilities are flagrant violations of international humanitarian law.
"Health workers have an obligation to treat the sick and injured without discrimination."
The international group Emergency runs health programmes in countries including Central African Republic, Iraq, Sudan and Afghanistan.
Luca Radaelli is in charge of its programs in Afghanistan and he said the charity has to work very hard to gain the trust of communities to help ensure their staff stay safe.
"Our way to manage security is our reputationâ€¦ we have to be absolutely neutral and provide a high level of healthcare free of charge for everyoneâ€¦ we don't ask questions about what side people are on."
He said Afghanistan desperately needed medics, as the number of war-related admissions in its centre in Kabul had more than doubled since 2010.
The WHO said 180 frontline health services in Iraq have been suspended due to fighting, leaving millions of people without any access to healthcare.
But health workers continue to put their lives on the line to get medical aid to those caught up in the violence.
Dr Roberts told me, as she continued to shelter from bombings overhead in Saada during our interview: "At the beginning you have a high level of stress. Then, even though the stress is still there, you become very accustomed to it.
"It's a choice I've made to come to these places.
"If don't come I don't know who will."
@TulipMazumdar
The World Health Organization is calling for "intensified action" to protect health workers treating people in crisis and conflict zone.