Transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders for which symptomatic, curative, or prophylactic treatments are not available. TSEs arise as a consequence of the conversion of soluble cellular prion protein (PrP(C)) into the scrapie isoform (PrP(Sc)), which aggregates and accumulates in the central nervous system. Proposed drugs against TSEs range from small organic compounds to antibodies; various therapeutic strategies have been proposed, including blocking the conversion of PrP(C) to PrP(Sc), increasing PrP(Sc) clearance, and/or stabilizing PrP(C). While several compounds have been effective in vitro and in animal models, none have proven effective in clinical studies to date. Such lack of in vivo efficacy is attributable to high compound toxicity and the lack of permeability of the selected compounds across the blood-brain barrier. In this review, we discuss recent advances in the screening and evaluation of organic compounds for anti-prion activity using multiple approaches, including initial screening in prion-infected cell cultures, in silico prediction of pharmacokinetic and physicochemical properties, ex vivo evaluation of cellular toxicity, and in vitro assays using purified recombinant prion proteins. The main challenges for effective discrimination of candidate lead compounds as therapeutic agents for TSEs, and the disadvantages of each screening strategy are discussed. We propose that a combination of in vitro, ex vivo, and in silico approaches would be useful for the rapid identification of novel anti-prion drug candidates with suitable pharmacokinetic and pharmacodynamic properties that would support their use as drugs.