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A correct soil moisture estimation is a fundamental prerequisite for many applications: agriculture, meteorological forecast, flood and drought prediction, and, in general, water accounting and management. Traditional methods typically provide point-like measurements, but suffer from soil heterogeneity, which can produce significant misinterpretation of the hydrological scenarios. In the last decade, cosmic-ray neutron sensing (CRNS) has emerged as a promising approach for the detection of soil moisture content. CRNS can average soil moisture over a large volume (up to tens of hectares) of terrain with only one probe, thus overcoming limitations arising from the heterogeneity of the soil. The present paper introduces the development of a new CRNS instrument designed for agricultural applications and based on an innovative neutron detector. The new instrument was applied and tested in two experimental fields located in Potsdam (DE, Germany) and Lagosanto (IT, Italy). The results highlight how the new detector could be a valid alternative and robust solution for the application of the CRNS technique for soil moisture measurements in agriculture.