To avoid problems associated with the storage and processing of newly developed potential medicines, there is a need to carry out thermal studies in the preclinical phase of drug development. The thermal behaviour and decomposition pathway of a whole novel class of patented potential molecular pharmaceutics, i.e., ethyl 2-[4-oxo-8-(R-phenyl)-4,6,7,8-tetrahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetates (1–6) were reported for the first time in inert and oxidative atmospheres. The experiments were conducted with the use of simultaneous thermogravimetry/differential scanning calorimetry (TG-DSC) and simultaneous thermogravimetry coupled with Fourier transform infrared spectroscopy (TG-FTIR). The decomposition pathways of compounds 1–6 were found to be different under oxidative and inert conditions. It was proven that the investigated molecules reveal higher thermal stability under a synthetic air atmosphere than under a nitrogen atmosphere, and their decomposition is preceded by the melting process. Among all the investigated compounds, only the meta-chloro derivative (4) was found to exhibit interesting polymorphic behaviour at a low heating rate (10 °C min−1). It was proven that the oxidative decomposition process of the studied molecules proceeds in three overlapping stages accompanied by strong exothermic effects. Additionally, it was concluded that the title compounds were stable up to a temperature of 195–216 °C in an atmosphere of synthetic air, and their thermal stability decreased in the order of R at the benzene ring: 4-CH3 > 3,4-Cl2 > 4-Cl > H > 2-OCH3 > 3-Cl.