Properties related to individual or bioactive compounds that constitute the matrix of pharmaceutical and natural drug products (e.g., essential oils, terpenoids, flavonoids, volatile compounds, and other chemicals) are present at low concentrations (e.g., parts per million or parts per billion). Classical separation, chromatographic, and spectrometric techniques such as high-performance liquid chromatography, gas chromatography, liquid chromatography, and mass spectrometry have been used for the elucidation of isolated compounds in research and development (R&D) of drugs and pharmaceutical products. Hence, the use of standard separation, chromatographic, and spectrometric methods were found useful for fingerprinting and comparing natural and synthetic samples, as well as for identifying single active compounds. However, these methods are time consuming and require some level of preprocessing of the sample before analysis. Over the last four decades, infrared (IR) spectroscopy became one of the most attractive and used methods for analysis of agricultural-related products and plant materials providing simultaneous, rapid, and nondestructive tool to quantify major constituents in such samples. This review describes the benefits and limitations of IR spectroscopy combined with multivariate data analysis for high-throughput screening and R&D of natural drugs and pharmaceutical products.