Flexible work arrangements (FWA) may be beneficial for increasing perceived flexibility (i.e. control over when, where and how to work) and reducing interference between work and private-life, but knowledge of gendered patterns of these relationships is sparse. Drawing on gender theory, the aim of this study was to conduct gender-differentiated analyses of the associations between FWA (non-regulated work or flex-time) and work–life interference using perceived flexibility as a mediator. Survey data were collected in 2016 from a sample of 2614 employees in the Swedish Transport Administration (response rate 67%). The sample included 39.6% women and 60.4% men, 71.7% had non-regulated work and 28.3% flex-time. Associations were determined using linear mixed models and mediation analysis. Results indicated a beneficial effect of non-regulated work (referencing flex-time) on work–life interference through an increase in perceived flexibility. The indirect effect of FWA was pronounced and statistically significant in the total sample, as well as in men and women. However, in men, non-regulated work was associated with a statistically significant increase in interference (competitive mediation). Gender did not interact significantly with work arrangement nor with perceived flexibility. In conclusion, the type of FWA can result in different perceptions of flexibility which in turn may affect experiences of work–life interference. Furthermore, it should be acknowledged that both FWAs and flexibility may be experienced differently for men and women regarding interference. Thus, employers seeking to reduce employee interference should consider gender norms and individual needs.