A straightforward methodology for the synthesis of isothiocyanate-functionalized mesoporous silica nanoparticles (MSNs) by exposure of aminated MSNs to 1,1′-thiocarbonyldi-2(1H)-pyridone is reported. These nanoparticles are chemically stable, water tolerant, and readily react with primary amines without the formation of any by-product. This feature allows the easy modification of the surface of the nanoparticles for tuning their physical properties and the introduction of gatekeepers on the pore outlets. As a proof-of-concept, amino-isothiocyanate-functionalized MSNs have been used for the design of a nanocontainer able to release the drug Ataluren. The release profile of the drug can be easily fine-tuned with the careful choice of the capping amine.