Christian charity Transforming Lives for Good says the lockdwon has produced many new challenges for children and their families, on top of problems which the Children's Commissioner highighted before coronavirus.
Charity Transforming Lives for Good (TLG) works with churches and vulnerable children on issues such as poverty, family breakdown and mental health.
The group are encouraging church members to appreciate how lockdown may have affected some families worse than other and to equip themselves for potentially dealing with emotional trauma that may have occured over the last six months.
Rae Morfin, TLG's head of therapeutic practice, told Premier: "Even before lockdown, for vulnerable children there were over 800,000 children living with domestic abuse and 1.6 million parents had real mental health issues - and that was before lockdown. So we know that when those children and those families are all enclosed that's only going to compound the issues."
The charity warns that the closing then gradual return of schools could have affected different children at varying times - with some struggling with the lack of social contact and possibly problems at home for half a year, and others dreading now going back into school each day if they have falled behind, have behavioural issues or were being bullied.
Rae Morfin explained: "Within the last two or three weeks of schools going back, we've been hearing of numbers of exclusions happening already...although it's familiar, there's new rules, there's new things that they've got to do and that does create anxiety for children. It's really about who's around them, which adults are around them to be able to help study them as they go back into school and deal with those anxieties."
She urged Christians to keep up their contact with children they know well - such as by doing video calls to see how they are - and encouraged churches to be open to talking about mental health with families this winter.
The charity is offering free online support to train church staff and volunteers in how to talk to young people about emotional wellbeing and is praying for families to know God's peace.