Pupils start back at Soham village college and St Andrew's primary next Monday and Tuesday, and the completion of checks is expected to reassure parents.
Ministers decided after the girls' deaths that school staff should be fully investigated before starting work, rather than just checked against the department's blacklist. They have now been forced into a U-turn because of the huge backlog (see story, left).
Ian Huntley, the college's former caretaker, is charged with the 10-year-olds' murders, while his partner Maxine Carr, a former classroom assistant at St Andrew's, has been charged with perverting the course of justice.
Howard Gilbert, head of Soham college, said it plans to ensure pupils waiting for lifts or buses home after lessons are properly supervised, following concerns raised in meetings with parents. Many pupils travel to the town from outlying villages.
Parts of the school grounds are sealed off but, he said, contractors, local businesses and local education authority personnel "have been wonderful" in getting the school prepared for the new term.
Counsellors will be on hand if needed, but he is hoping staff and pupils will have time to "find their feet and get back to reality".
Jessica's mother Sharon showed her support for a return to normality when it emerged she plans to return to her job as a classroom assistant at St Andrew's.
However, parents elsewhere have been taking drastic steps to protect their children. Paul and Wendy Duval, from Reading, are planning to have their 11-year-old daughter Danielle fitted with a microchip in her arm so she can be traced if abducted.
And two Shropshire mothers have issued 30 children with personal attack alarms. Kerry Poole, a governor at West Felton Church of England primary in Oswestry, and Gina Bright want alarms for all local children.
Ms Bright said: "We contacted police for advice on a trial run. The Jessica and Holly incident was very frightening and we believe children walking home need protection.
"This alarm will be heard from inside cars and houses. Hopefully someone would come and help."
However, a spokeswoman for the National Society for the Protection of Children said cases like that of Holly and Jessica are very rare: youngsters are most at risk of harm from their own parents or carers.