Previous research has consistently found an association between elevated anxiety and school refusal behaviour (SRB) in children and young people. Kearney (J Child Psychol Psychiatry 48:53–61, 2007) suggested that this relationship is best understood by exploring motivations underlying SRB. The present study aimed to establish whether motivating factors associated with non-attendance could explain the relationship between trait anxiety and school attendance in a community sample of 162 12–13-year-old young people. We measured motivating factors using the School Refusal Assessment Scale-Revised (SRAS-R; Kearney in J Psychopathol Behav Assess 24:235–245, 2002). In addition, we assessed the factor structure of the SRAS-R using confirmatory factor analysis. Goodness-of-fit indices supported a three-factor model highlighting motivational factors related to negative affect, social avoidance and attention-seeking. The results showed a negative relationship between trait anxiety and school attendance that was mediated by social avoidance and attention-seeking. We suggested that a consideration of motivating factors is important to understand and address anxiety-related non-attendance in young people.