This paper proposes a workflow to assess the uncertainty of the Normalized Difference Vegetation Index (NDVI), a critical index used in precision agriculture to determine plant health. From a metrological perspective, it is crucial to evaluate the quality of vegetation indices, which are usually obtained by processing multispectral images for measuring vegetation, soil, and environmental parameters. For this reason, it is important to assess how the NVDI measurement is affected by the camera characteristics, light environmental conditions, as well as atmospheric and seasonal/weather conditions. The proposed study investigates the impact of atmospheric conditions on solar irradiation and vegetation reflection captured by a multispectral UAV camera in the red and near-infrared bands and the variation of the nominal wavelengths of the camera in these bands. Specifically, the study examines the influence of atmospheric conditions in three scenarios: dry-clear, humid-hazy, and a combination of both. Furthermore, this investigation takes into account solar irradiance variability and the signal-to-noise ratio (SNR) of the camera. Through Monte Carlo simulations, a sensitivity analysis is carried out against each of the above-mentioned uncertainty sources and their combination. The obtained results demonstrate that the main contributors to the NVDI uncertainty are the atmospheric conditions, the nominal wavelength tolerance of the camera, and the variability of the NDVI values within the considered leaf conditions (dry and fresh).