Spherical, individual polymer nanoparticles with functional –SH groups were synthesized via aerosol photopolymerization (APP) employing radically initiated thiol-ene chemistry. A series of various thiol and alkene monomer combinations were investigated based on di-, tri-, and tetrafunctional thiols with difunctional allyl and vinyl ethers, and di- and trifunctional acrylates. Only thiol and alkene monomer combinations able to build cross-linked poly(thio-ether) networks were compatible with APP, which requires fast polymerization of the generated droplet aerosol during the photoreactor passage within a residence time of half-minute. Higher monomer functionalities and equal overall stoichiometry of functional groups resulted in the best nanoparticles being spherical and individual, proven by scanning electron microscopy (SEM). The presence of reactive –SH groups in the synthesized nanoparticles as a basis for post-polymerization modifications was verified by Ellman’s test.