The poultry sector contributes four percent to the national GDP of Nepal. However, this sector is under threat with periodic outbreaks of Avian Influenza (AI) subtypes H5 and H9 since 2009. This has been both a public health threat and an economic issue. Since the past few years, outbreaks of AI subtype H9 have caused huge economic losses in major poultry producing areas of Nepal. However, the risk factors associated with these outbreaks have not been assessed. A retrospective case-control study was conducted from April 2018 to May 2019 to understand the risk factors associated with AI subtype H9 outbreaks in Kathmandu valley. Out of 100 farms selected, 50 were “case” farms, confirmed positive to H9 at Central Veterinary Laboratory, Kathmandu, and another 50 farms were “control” farms, matched for farm size and locality within a radius of three km from the case farm. Each farm was visited to collect information using a semi-structured questionnaire. Twelve potential risk factors were included in the questionnaire under the broad categories: birds and farm characteristics, and management and biosecurity status of the farms. Univariable and multivariable logistic regression analysis was conducted and corresponding odds ratios were calculated. Risk factors, associated with AI subtype H9 outbreaks in Kathmandu valley, identified in the final multivariable model were: “farms that have flock size greater than median flock size of study farms (>1500)” (OR = 4.41, 95% CI: 1.53-12.71, p = 0.006), “farms that did not apply rules to wear boots for visitors inside the farms” (OR = 4.32, 95% CI: 1.52-12.29, p = 0.006) and “other commercial farms located within one km periphery” (OR = 10, 95% CI: 1.8-50, p = 0.007). This study showed that outbreaks of AI subtype H9 in Kathmandu valley were associated with a higher population of birds in the farm, poor management practices, and weak biosecurity measures in poultry farms. We suggest improving management practices and increase biosecurity in the farms to reduce incidences of AI subtype H9 outbreaks in Kathmandu valley.