•Gender differences affect transport mobility choices in Jakarta and Kuala Lumpur.•Perception of safety is spatially and socio-culturally constructed.•Women are more likely to report negative perceptions of safety as compared to men.•Multidisciplinary perspectives is required to understand gendered mobility. Despite numerous studies on how gender differences affect transport mobility choices and perception of safety, there has been little emphasis on the influence of spatial and socio-cultural constructs on it, particularly in the Southeast Asian context. This article investigates this relation through (1) an on-street survey involving 383 participants in eight neighbourhoods in Jakarta and Kuala Lumpur, (2) analysing videos taken with the walking with video approach, and (3) a computational analysis of the street network using space syntax. Findings suggest that a large proportion of women ascribed to negative perceptions of safety as compared to men. Negative perceptions of safety were related to wariness towards motorcycles in Jakarta and absence of other pedestrians and the image of the place in Kuala Lumpur. This difference can be attributed to distinctions in spatial configurations and socio-cultural constructs between both cities. Findings provide practical insights – mode segregation or changes to street design – to address gendered mobility for sustainable urban transport in the region.