A novel series of thiazolium ionic liquids (TILs) bound to chloride (2a–c), tetrafluoroborate (BF4) (3a–c), and bis-(trifluoromethanesulfonimide) (Tf2N) anions (4a–c) was synthesized and their physicochemical characteristics were investigated using various microanalytical techniques. The pharmacological potential of the new TILs was assessed as chemotherapeutic agents for bacterial infections and ovarian cancer (SKOV-3). Notably, ILs with the same cations become more bactericidal upon their binding with the strongest chaotropic anion (TN2f). The in vitro toxicity of the TILs toward ovarian carcinoma cell lines (SKOV-3) and normal human skin fibroblast cells (HSF) revealed that all tested TILs have the capacity to induce a dose- and time-dependent decline in SKOV-3 cell viability, with Tf2N-linked TILs (4a–c) having a preferable efficacy. In addition, the new compounds showed excellent selectivity for cancer cells (SKOV-3) over healthy cells (HSF). [iPBzTh][Tf2N] (4b) is the most cytotoxic and specific one and may act as a promising anti-ovarian cancer agent.