Against the background of divergent political developments across Europe, farm animal welfare (FAW) science has evolved during the last three decades as an inter-disciplinary research area. Recent achievements include pan-European research projects and the implementation of animal welfare assessment systems on-farm. The aim of this study was mapping activities for FAW science and investigating geographical differences in FAW research in Europe (EU28 + candidate countries and the European Economic Area) with regard to available resources (e.g. human resources, infrastructure, funding) and research output (e.g. collaborations and publications). Further, we enquired if economic attributes such as the Coefficient of National Innovation Capacity (NIC) were associated with the reported available resources and research output factors (publications and collaborations) of FAW research. Based on questionnaires sent out to a wide researcher network in regions of an enlarged Europe, we found differences with regard to ‘input factors’ such as human resources, animal and laboratory facilities and national and international research funding and ‘output factors’ such as inter/national collaboration, participation in EU-funded projects related to FAW and number of publications. Respondents were allocated to 4 Western and 4 Eastern geographical clusters of countries (‘hubs’). There were a larger number of researchers, students and technical staff per laboratory in Western compared to Eastern hubs. A pronounced difference was found for funding, as 35% of respondents in the Eastern hubs stated that they lack funded FAW projects compared to 4% in the West. In general, respondents from the Western hubs stated significantly more often that they run projects in the field of FAW research (p = 0.034). Furthermore they were significantly more involved in EU-funded schemes, such as FP7 (EU’s Research and Innovation Funding Programme for 2007–2013) with 24% (p = 0.013) and in ERA-NET Cofund projects (European Research Area—Coordination of Research Programmes) with 5.7% (p = 0.042). The average sum of impact factors from 5 self-named citations was 3.0 ± 2.8 (mean, SD) in the Eastern hubs and 7.5 ± 4.4 in the Western Hubs. When investigating associations of the economic status of EU countries with resource factors and achievements in FAW research, the ‘Coefficient of National Innovation Capacity (NIC)’ was moderately correlated with the input factors for FAW research such as the average number of PhDs currently employed in the institutions (r_s = 0.66; p < 0.001) and the total number of employed researchers (r_s = 0.56; p < 0.01). Stronger associations were found between the scientific output and the economic ranking, here represented by the cumulative impact factor of their published papers (r_s = 0.74; p < 0.001), and between the number of EC-project reports published in CORDIS 2015 with NIC (r_s = 0.67; p < 0.001). We conclude that due to economic disadvantages as represented by the lower NIC or rare participation in EU-funding schemes, the Eastern Hubs could not reach the same level of output factors as the Western Hubs, which negatively impacts on the number of young researchers (PhDs) and impact factors, thus resulting in lower visibility and influence.