Many phosphorylated nucleoside derivatives have therapeutic potential, but their application is limited by problems with membrane permeability and with intracellular delivery. Here, we prepared polypyrrole microvessel structures modified with superparamagnetic nanoparticles for use as potential carriers of nucleotides. The microvessels were prepared via the photochemical polymerization of the monomer onto the surface of aqueous ferrofluidic droplets. A complementary physicochemical analysis revealed that a fraction of the nanoparticles was embedded in the microvessel walls, while the other nanoparticles were in the core of the vessel. SQUID (superconducting quantum interference device) measurements indicated that the incorporated nanoparticles retained their superparamagnetic properties; thus, the resulting nanoparticle-modified microvessels can be directed by an external magnetic field. As a result of these features, these microvessels may be useful as drug carriers in biomedical applications. To demonstrate the encapsulation of drug molecules, two labeled mRNA cap analogues, nucleotide-derived potential anticancer agents, were used. It was shown that the cap analogues are located in the aqueous core of the microvessels and can be released to the external solution by spontaneous permeation through the polymer walls. Mass spectrometry analysis confirmed that the cap analogues were preserved during encapsulation, storage, and release. This finding provides a foundation for the future development of anticancer therapies and for the delivery of nucleotide-based therapeutics.