Owing to restrictions of the COVID-19 pandemic, increased stress is evident in university students with a lifetime history of non-suicidal self-injury (NSSI). Therefore, we examined two groups of university students (n = 174) in an online survey, one that exhibited early NSSI in adolescence (n = 51) and another that exhibited continuous NSSI beyond the age of 18 (n = 123) (German Clinical Trials Register DRKS00023731). We compared the two groups in terms of depressive symptoms in the previous 2 weeks as well as self-perceived changes in emotional burden, urge to self-injure and NSSI frequency in the first year of the pandemic compared with the year before (pre-pandemic). Among other findings, both groups showed an increase in emotional burden and urge to self-injure.