In this paper we contribute to the emerging literature on the effect of the COVID-19 pandemic on the gender gap in research productivity. We extend previous studies by considering men and women academics from science and non-science disciplines through an analysis of data from academics at 14 universities across two countries (seven in Australia and seven in Canada) and focusing on the role of primary caregiving. Our empirical approach used logistic regressions and the Blinder–Oaxaca decomposition technique. The latter enabled us to ask: ‘How much of the gender gap in perceived productivity during the pandemic is due to gender differences in primary care responsibilities?’ Within the sample (N = 2,817) of academics, 33% of women and 25% of men reported that their perceived publication ability decreased a lot during the pandemic. This is an eight percentage-point gender gap in perceived publication ability. Statistical analysis revealed that two-fifths (40%) of this gap may be explained by gender differences in having primary responsibility for the care of children. Gender differences in other characteristics such as age, discipline, and increased teaching and administrative work were not, as a group, significant. There were also no differences between Australia and Canada. The findings are important, particularly for the pursuit of gender equality within academia. In the absence of specific mitigating interventions, research disruptions in 2020 may have long-lasting career scarring effects (e.g. hiring, promotion, tenure) and, as a result, see women further disadvantaged within the academy.