It will be the robot's first foray into healthcare after previous deployments in shopping centres, banks and train stations.
One hospital plans to deploy more robots over the next 10 years.
Some experts have questioned the usefulness of social robots such as Pepper.
Softbank, the company behind Pepper, and partner French robotics firm Aldebaran have seen huge success with the creation, with each batch of 1,000 selling out fast in Japan.
The hospital-based robots will be significantly more expensive than the $1,850 basic model with a $34,000 (Â£24,000) price tag.
This will include specially designed software from Belgian firm Zora Bots, as well as access to the helpdesk should issues arise when Pepper is on duty.
The 1.2m (4ft) tall robot can recognise the human voice in 20 languages and can detect whether it is talking to a man, woman or child.
In the CHR Citadelle hospital in Liege, Pepper will remain in the reception area but, at the AZ Damiaan hospital in Ostend, it will accompany visitors to the correct department.
The Liege hospital wants to become one of the world's most futuristic over the next 10 years.
"It's about architecture, future rooms and robots, the ones we already have and the ones we're going to get," said CHR Citadelle's communication director Nathalie Evrard.
Both hospitals already use the smaller Nao robots, also made by Softbank, in both their paediatric and geriatric wards.
The little robots assist in exercise sessions and help children overcome their fears of surgery, sometimes going to the theatre with them.
Some remain sceptical about how useful Pepper can be in both homes and commercial settings, with robotics expert Prof Noel Sharkey previously telling the BBC: "It is good at conveying human-like gestures but the way it detects human emotions might be over-hyped."

The first minister said images of Aylan Kurdi being carried from the sea had "touched our hearts".
Ms Sturgeon is to convene a migrant crisis summit on Friday with councils and humanitarian agencies.
Prime Minister David Cameron has come under increasing pressure for Britain to accept more refugees.
Scottish Conservative leader Ruth Davidson is among those who have urged Mr Cameron to do more to tackle the refugee crisis in Europe.
But Immigration Minister James Brokenshire said accepting more refugees was not the answer.
Speaking at First Minister's Questions, Ms Sturgeon said: "As first minister I pledge that I will ensure Scotland will do everything possible to help in this refugee crisis.
"I will be far from the only person reduced to tears last night at the picture of a little boy washed up on a beach.
"That wee boy has touched our hearts but his is not an isolated tragedy.
"He and thousands like him whose lives are at risk is not someone else's responsibly; they are the responsibility of all of us.
"So yes I am angry, I am very angry at the walk-on-by attitude of the UK government and I implore David Cameron to change his position and change it today.
"I pledge as first minister of this country that we stand ready to offer sanctuary to refugees that need our help."
Scottish Labour leader Kezia Dugdale also criticised Mr Cameron's response to the crisis.
She urged the first minister to "convene an urgent meeting with Scotland's council leaders, party leaders and people in this parliament and other relevant government agencies so that Scotland can speak with one voice and match our compassion with the action we are all willing to take".
Ms Sturgeon said she had already set up a summit, which will bring together humanitarian organisations, including the Scottish Refugee Council, leaders of councils, civic organisations and religious leaders.
Scottish Liberal Democrat leader Willie Rennie said he would accept the invitation to attend the summit.
Ms Davidson said the UK government must act "closer to home" and go beyond donating aid to Syria, adding: "This is not an immigration issue - it's a humanitarian crisis."
She added: "I call on David Cameron to lead our government's response and accept more refugees."
Pepper, the humanoid robot programmed to "understand" human emotions, is to take a new job - as a receptionist in two Belgian hospitals.
[NEXT_CONCEPT]
Nicola Sturgeon has told how she was reduced to tears by photos of a dead Syrian boy washed up on a Turkish beach.