Low pathogenic avian influenza (LPAI) of subtype H9 outbreaks have been frequently occurring in major commercial hubs of Nepal including Chitwan, a central lowland area, causing substantial economic losses to the farmers. However, the risk factors associated with these outbreaks have been poorly understood, and hence, this case-control study was conducted in Chitwan, Nawalpur, and Makawanpur districts of Nepal from October 2019 to March 2020. A total of 102 farms were selected in which 51 were case farms, and 51 were controls. Case farms were avian influenza (AI)-subtype-H9-confirmed farms through polymerase chain reaction (PCR) assays on poultry samples. Control farms included farms that were AI-negative in the antigen test brought to the National Avian Disease Investigation Laboratory, Chitwan, for diagnosis during the study period. Each farm was visited to collect information using a semi-structured questionnaire. A total of 25 variables representing farm characteristics and biosecurity measures were considered as potential risk factors. The final multivariable model showed that distance of less than 0.5 km from the main road (OR = 4.04, 95% CI = 1.20–13.56, p = 0.023), distance of less than 1 km from a nearest infected farm (OR = 76.42, 95% CI = 7.17–814.06, p = 0.0003), and wild birds coming around the farm (OR = 6.12, 95% CI = 1.99–18.79, p = 0.0015) were risk factors for avian influenza type H9, whereas using apron or separate cloth inside the shed (OR = 0.109, 95% CI = 0.020–0.577, p = 0.0092) was shown to reduce the risk of farms being positive for AI subtype H9. These findings suggest that due consideration should be given to site selection while establishing the farms and the importance of implementing appropriate biosecurity measures, such as using separate cloth inside the shed and preventing the entry of wild birds inside the farm to reduce the potential risk of introduction of avian influenza type H9 to their poultry farms.