Background: Bacillary dysentery (BD) is an acute bacterial infection of the intestine caused by Shigella spp., with clinical symptoms ranging from fever to bloody diarrhoea to abdominal cramps to tenesmus. In Vietnam, enteric bacterial pathogens are an important cause of diarrhoea and most cases in children under 5 years of age are due to Shigella strains. The serogroups S. flexneri and S. sonnei are considered to be the most common. The main objective of this study was to, for the first time, assess the seasonal patterns and geographic distribution of BD in Vietnam, and to determine the climate risk factors associated with the incidence of BD in Kon Tum Province, where the highest rate of bacillary dysentery was observed from 1999 to 2013. Methods: The seasonal patterns and geographic distribution of BD was assessed in Vietnam using a seasonaltrend decomposition procedure based on loess. In addition, negative binomial regression models were used to determine the climate risk factors associated with the incidence of BD in Kon Tum Province, from 1999 to 2013. Results: Overall, incidence rates of BD have slightly decreased over time (except for an extremely high incidence in 2012 in the north of Vietnam). The central regions (north/south central coast and central highlands) had relatively high incidence rates, whereas the northwest/east and Red River Delta regions had low incidence rates. Overall, seasonal plots showed a high peak in the mid-rainy reason and a second smaller peak in the early or late rainy season. The incidence rates significantly increased between May and October (“wet season”) across the country. In Kon Tum Province, temperature, humidity, and precipitation were found to be positively associated with the incidence of BD. Conclusions: Our findings provide insights into the seasonal patterns and geographic distribution of BD in Vietnam and its associated climate risk factors in Kon Tum Province. This study may help clinicians and the general public to better understand the timings of outbreaks and therefore equip them with the knowledge to plan better interventions (such as improving water, sanitation, and hygiene conditions) during peak seasons. This can, in turn, prevent or reduce outbreaks and onwards transmission during an outbreak.