Cambridgeshire County Council has opened a phone service from 0800 BST on Monday.
The community has been shattered by the news that bodies found in discovered in woods in Lakenheath in Suffolk are almost certainly those of the 10-year-old friends.
Hundreds of people have sought comfort at church services in Soham, in Cambridgeshire, where flowers and tributes to the girls have been left.
The counselling facility is being limited to the pupils at the local schools, their parents and staff which could run to several thousand people.
There are two primary schools in Soham, each with 400 children, and 1,300 pupils attend the village college.
Trained counsellors will be available from the county council's education and social services departments.
Payne inquiry
A council spokesman says experience from the Sara Payne inquiry shows some people may just want to talk to somebody about their feelings.
Others may want to refer a member of their family or a close friend for help, he said.
Alison Palmer, a governor at Holly and Jessica's school, says counselling is vital.
"Young and old alike are feeling this," she said.
"People who know the family, people who don't, people who are connected with the school people who aren't.
"That is why it is so important for us to have this support both in the short term and in the very, very long term."
The families of both girls have asked for their privacy to be respected and police said it may be days before the girls' bodies are formally identified.
Helpline number
Detectives have also been granted a 36-hour extension to continue questioning Soham college caretaker Ian Huntley, 28, and his girlfriend Maxine Carr, 25.
Mr Huntley is being held on suspicion of abducting and murdering Holly and Jessica.
Ms Carr, a teaching assistant in the girls' class last term, was arrested on suspicion of murdering them.