We assessed genetic and environmental influences on social isolation across childhood and the overlap between social isolation and mental health symptoms including depression symptoms, conduct problems, and psychotic-like experiences from adolescence to young adulthood. Participants included 2,232 children from the Environmental Risk Longitudinal Twin Study. Social isolation was measured at ages 5, 7, 10, 12, and 18. A Cholesky decomposition was specified to estimate the genetic and environmental influences on social isolation across ages 5, 7, 10, and 12. An independent pathway model was used to assess additive genetic (A), shared environmental (C), and non-shared environmental (E) influences on the overlap between social isolation and mental health problems from age 12 to 18. Genetic and non-shared environmental influences accounted for half of the variance in childhood social isolation. Genetic influences contributed to the continuity of social isolation across childhood, while non-shared environmental influences were age-specific. The longitudinal overlap between social isolation and mental health symptoms was largely explained by genetic influences for depression symptoms (r = 0.15-0.24: 82-84% A, 11-12% C, and 5-6% E) and psychotic-like experiences (r = 0.13-0.15: 81-91% A, 0-8% C, and 9-11% E) but not conduct problems (r = 0.13-0.16; 0-42% A, 42-81% C, 16-24% E). Our findings emphasise that rather than a risk factor or an outcome, social isolation is aetiologically intertwined with the experience of poor mental health. An integrative assessment of social isolation could be a helpful indicator of underlying mental health symptoms in young people.