Having cancer in childhood is a risk factor for separation anxiety symptoms, with negative effects on the disease and psychological wellbeing. The Covid-19-pandemic-related concerns could have a negative effect. The present study explores the interplay between separation anxiety symptoms and COVID-19-related worries in pediatric cancer patients and their mothers, compared to a group of healthy children and their mothers, during the pandemic. Thirty-three subjects with cancer, aged 7–15 years, and their mothers were compared to a control sample of 36 healthy children and caregivers. They were administered a pandemic-related psychological experience survey and standardized questionnaires assessing psychological wellbeing, anxiety, and separation anxiety symptoms. Children with cancer reported significantly higher prosocial behaviors, fear of being alone, and fear of abandonment. Their mothers had worse psychological wellbeing, higher COVID-19 concerns, anxiety, and separation anxiety symptoms. The multiple linear regression model showed that an increase in children’s separation anxiety symptoms was associated with younger age, more recent diagnosis, more mother-child time, lower mothers’ worry for children’s contagion, and higher mothers’ and children’s anxiety. COVID-19-related worries of clinical children’s mothers seem to be protective for children’s psychological wellbeing. Early psychosocial support interventions for mothers are essential in health services for cancer.