Venturi has long been an attractive method of measuring flow rate in a variety of engineering applications since pressure loss is relatively small compared with other measuring methods. The current study focuses on making detailed uncertainty estimations as the upstream flow disturbance affects uncertainty levels of the flow rate measurement. Upstream flow disturbance can be determined by 9 different swirl generators. Measurement uncertainty of flow rate has been estimated by a quantitative uncertainty analysis which is based on the ANSI/ASME PTC 19.1-2005 standard. The results of flow rate uncertainty analysis show that the case with systematic error has higher than that without systematic error. Especially the result with systematic error exhibits that the uncertainty of flow rate was gradually increased by swirl flow disturbance. The uncertainty of flow rate measurement can be mainly affected by differential pressure and discharge coefficient. Flow disturbance can be also reduced by increasing of the upstream straight length of Venturi.