Students are facing more than standard back-to-school anxiety this fall.

Returning to classrooms after a year of remote learning and a continuing pandemic, some children may have difficulties coping emotionally with all the changes. From separation anxiety to the need for support, health experts say parents should be on the lookout for behaviors that may signal anxiety and stress.

Children are already starting the year with more challenging mental-health needs than in years past. Students around the country showed a 30% to 40% uptick in emotional risk over the past year, according to estimates reviewed by Nathaniel von der Embse, co-director of the School Mental Health Collaborative at the University of South Florida, which conducts research with some of the country’s largest school districts. Children who report emotional risk display fewer behaviors that demonstrate emotional coping than those that are considered emotionally healthy, according to Dr. von der Embse.

For parents trying to ensure a smooth start to the school year, it is difficult to know when—or how—to intervene, Dr. von der Embse says.

“Parents should trust their intuition…knowing what is significantly different from their child’s behavior rather than focusing on external expectations,” Dr. von der Embse says. He added that there is no universal predictor of behavior or social-emotional indicators that a child needs intervention.

Here are some things parents should be watching, according to psychology professionals:

Consider Red Flags

When Lauren Eskra’s son and daughter, both early teens, went back to in-person school for the first time in 18 months, she was unsure how they’d adjust after so much time at home.

“They need to relearn how to interact with someone in person,” says Ms. Eskra, who lives in Miami.

Others may experience separation anxiety—especially youngsters attending in-person school for the first time—which can manifest in different ways, says Dominika Nolan, a therapist at the Center for Child Counseling in Palm Beach Gardens, Fla. Some children might throw morning tantrums about not wanting to leave parents behind, while others may cling to caregivers when seeing them each afternoon.

“Always make sure to reassure them that you’re safe and you’re OK while they’re at school,” she says.

“‘A lot about how the child perceives [the transition] has to do with how the parent perceives it.’”

— Dr. Kate Eshleman, a pediatric psychologist

Keep an eye on physical symptoms in younger children. Children under about 9 years old are more likely than older children to complain of headaches or stomachaches when experiencing anxiety, says Dr. Kate Eshleman, a pediatric psychologist at Cleveland Clinic Children’s. Sudden bed-wetting or a lack of appetite can be a normal sign of adjustment unless it becomes ongoing, she adds.

Children in junior high and high school are less forthcoming when signaling distress. “Older children tend to internalize things,” says Dr. Eshleman. That means parents must keep an eye out for changes in appetite, mood and the amount of time they spend online. On school nights, spend time together in person rather than allowing them to slip away to their rooms.

“At the end of the day, let them know you are thinking about them,” she says.

Offer Support

There are many ways that parents can offer support. Start by acknowledging emotions that your child is feeling while arming them with ways to better explain their feelings, says Abigail Gewirtz, a child psychologist and author of “When the World Feels Like a Scary Place.”

For instance, if a younger child has tears in their eyes, it is a good time to acknowledge that they may be feeling sad as well as frustrated, she says. Other times parents can show their child that they recognize their feelings and would feel similar in that kind of stressful situation.

“Validate their emotions by helping them identify and label them,” Dr. Gewirtz says.

Talk About the Pandemic

Discussing the ways Covid-19 has changed the school environment and how to treat others with different experiences has helped Rachel Nix smooth the transition for her daughters, who started school in August. Ms. Nix is making sure to speak with them—ages 7, 11 and 12—about even the smallest changes, including how to be polite when someone next to them coughs.

“I said, ‘Don’t be bullies—we’re nice,’” says Ms. Nix, a radio personality in Lemoore, Calif.

Addressing inconsistent masking and other safety protocols with your child helps too, says Dr. von der Embse. The resurgence of the Delta variant means that children in recent months have been processing mixed messages, which can increase stress at school. Differences between pandemic protocols in school and at-home—including mask wearing—can add to confusion of how one is expected to act and detract from learning.

If some children seem more closed off during the transition, use open-ended questions to spark conversations rather than asking “How was school?” says Dr. Eshleman. Ask them to recap a funny moment from lunch or what they enjoyed about a particular class to get them talking. Allowing children time to reply and talk can make it easier for them to open up about other issues, she adds.

When to Seek Help

While most stress-related behaviors will settle after a two or three-week adjustment period, some children will require more attention, Dr. Eshleman says. Sustained changes that are impacting their ability to function could be a sign of something more serious, she says.

Slipping grades, sleeping in class or withdrawal from everyday activities signal the need to get others involved. Start by working with teachers to get more information about your child’s behavior in school.

When seeking out additional resources, a parent’s positive attitude is key. Many times, an adult’s anxiety over the start of the year can be reflected in the student’s mental well-being, says Dr. Eshleman. “A lot about how the child perceives [the transition] has to do with how the parent perceives it,” she says.

Write to Alina Dizik at alina.dizik@wsj.com