The pharmaceutical sector is a flagship of the economy in most developed countries and is one of the most research-intensive sectors of modern economies. The aim of this paper was to determine the mutual relationships between the research and development (R&D) resources, various indicators of scientific performance and the competitiveness of the sector. We carried out a cointegration analysis of a time series of R+D resources, the number of academic papers published, as well as patents and the competitiveness of this sector in various developed states. The econometric analysis of time series is built on panel cointegration models. Based on the combination of different comprehensive and coherent international databases and applying the latest methods of modern time series analysis, the paper proves that, in most developed countries, a direct, significant, causal, lagged relationship between the monetary resources allocated to R&D and the number of academic papers, as well as the number of patents can be observed. In most cases, a causal relationship can be demonstrated between the number of academic papers and patents, but vice versa, this fact is not provable. This study highlights the complexity of innovation systems in the pharmaceutical sector. The results prove only a weak connection between the number of patents and the number of publications. When evaluating the efficiency of the utilisation of resources allocated to pharmaceutical R+D, the effect of the time lag should be considered.