Individuals diagnosed with autism spectrum disorder (ASD) are more likely to have suicidal thoughts and behaviors. However, little research delineates the temporal and mechanistic associations between potential risk factors and suicidality in autistic individuals. We assessed 129 autistic and 121 age-matched and sex-assigned-at-birth-matched typically developing (TD) children and youth at baseline and follow-up. We evaluated internalizing/externalizing problems, bullying experiences, and three executive function tasks at a mean baseline age of 13.4 years (standard deviation: 4.2 years). After an average of 5.8 years (standard deviation: 1.7 years), we evaluated their suicidal thoughts and behaviors. The experiences of being bullied partially mediated the temporal relationship between pre-existing ASD and later-reported suicidal thoughts. Several cognitive flexibility and sustained attention indices mediated the temporal relationship between pre-existing ASD and later-reported suicidal thoughts. A multiple mediation model confirmed that bullying victimization and cognitive flexibility jointly mediated the temporal relationship between ASD and suicidal thoughts. Better cognitive flexibility and experiences of bullying victimization in autistic children/youth were both associated with higher risks of later-reported suicidal thoughts in adolescence/adulthood. School bullying-prevention programs and tailored clinical support for autistic youth with better cognitive flexibility are warranted for personalized suicide prevention for the autistic population.