Abstract Agriculture is the mainstay of livelihoods of the rural Bangladeshi population with the majority involved in the staple rice production which is subjected to seasonal variation. Rice production is invariably related to food insecurity which translates to the food shortage or lean periods. In order to have a comprehensive view on food insecurity in Bangladesh, it is necessary to assess the seasonality of food insecurity status and the factors associated with it. The objective of this paper is to compare the effect of two major rice harvest seasons and the post-aus rice harvest period on household food insecurity along with the contribution of relevant household characteristics. Data was collected during Bangladeshi aman harvest (November–January) and boro harvest (April–June) seasons and post-aus harvest (September–October) period. Information of 47,239 households from February 2011 to November 2013 was subjected to bivariate and multivariate analyses and statistical significance was declared when p < 0.05. Around 27%, 47%, and 26% of households were food insecure during aman harvest, boro harvest, and post-aus harvest period respectively. The aman harvest [adjusted OR (aOR): 0.54 [95% CI: 0.40–0.74; p < 0.001] and post-aus [aOR: 0.59 [95% CI: 0.44–0.80; p < 0.001] period had a lower odds of being food insecure when compared to boro harvest season except for the northern Rangpur region. Contrary to expectation, the prevalence of household food insecurity in the defined seasons is less during post-aus harvest period (the perceived lean period) and aman harvest season in comparison to the boro harvest season when food and work is more readily available in rural Bangladesh. There are several statistically significant household characteristics, namely household head being a farmer, educational status of household head, and household monthly income to have higher impact on food insecurity.