The aim of this study was to examine whether the relationship between a set of risk and protective factors (e.g., self-esteem, stress, intolerance of uncertainty, autistic symptoms) and mental health problems differed between autistic and non-autistic undergraduates enrolled in UK universities across genders. Autistic and non-autistic undergraduates were invited to complete an online survey between November 2022 and June 2023. The sample included 226 autistic participants, mean age = 21.36, SD = 4.04, and 46.9%, and 521 non-autistic participants, mean age = 21.96, SD = 4.24, and 63.3%. Two-way ANOVA followed by post-hoc comparisons were used to examine gender differences in mental health problems and multiple regression models were used to identify the predictors of mental health problems among autistic participants in comparison to non-autistic participants. A higher number of autistic undergraduates self-reported having mental health diagnoses than non-autistic undergraduates. Autistic females and autistic and non-autistic individuals of genders other than male or female had increased suicidality-defined to include both suicidal ideation and behaviours - relative to some groups. There were no gender differences in anxiety and worry, and in behavioural symptoms of depression and anxiety. Moreover, for both autistic and non-autistic participants, intolerance of uncertainty was associated with higher levels of anxiety and worry, whereas resilience was associated with lower levels of suicidality and behavioural symptoms of depression and anxiety. While autistic undergraduates self-reported more mental health disorders, there were more similarities than differences between autistic and non-autistic undergraduate students in terms of mental health risk and protective factors.