The metrological performance of a virtual flowmeter-based transducer for monitoring helium under cryogenic conditions is assessed. At this aim, an uncertainty model of the transducer, mainly based on a valve model, exploiting finite-element approach, and a virtual flowmeter model, based on the Sereg-Schlumberger method, are presented. The models are validated experimentally on a case study for helium monitoring in cryogenic systems at the European Organization for Nuclear Research (CERN). The impact of uncertainty sources on the transducer metrological performance is assessed by a sensitivity analysis, based on statistical experiment design and analysis of variance. In this way, the uncertainty sources most influencing metrological performance of the transducer are singled out over the input range as a whole, at varying operating and setting conditions. This analysis turns out to be important for CERN cryogenics operation because the metrological design of the transducer is validated, and its components and working conditions with critical specifications for future improvements are identified.