Nanoemulsion-templated long sustained polyelectrolyte (PE) nanocapsules (average size < 200 nm) loaded with Oil Red O and two cyanine-type photosensitizers: IR-786 and IR-780 were successfully fabricated by using the layer-by-layer (LbL) technique. All nanoproducts were subjected to in vitro release characteristics and analysis of selected control parameters, i.e., type of surfactant head group, characteristic release time and surfactant–polyelectrolyte interactions. Their properties were characterized by means of dynamic light scattering (DLS) compared with scanning electron microscopy (SEM) and atomic force microscopy (AFM). In our studies for construction of oil-in-water nanoemulsion templates we selected three cationic surfactants with different nature of hydrophilic head groups, i.e., double-headed (or so-called dicephalic-type) N,N-bis[3,3′(trimethylammonio)propyl]dodecanamide dimethylsulfate (C₁₂(TAPAMS)₂), bulky saccharide-derived 2-(dodecyldimethylammonio)ethylglucoheptonamide bromide (D₂GHA-12) and a classic dodecyltrimethylammonium bromide (DTABr) for comparison. The polyelectrolytes were the following: polyanion of poly(sodium 4-styrenesulfonate) (PSS) and polycation of poly(diallyldimethylammonium chloride) (PDADMAC). The in vitro release profile features, studied spectrophotometrically, were interpreted in the framework of diffusion-controlled processes and stability of the first interfacial PE–surfactant complex. Accordingly, the multicharge and bulky structure of the surfactant are found to be the most desirable factors for fabrication of long sustained and stable nanocapsules encapsulating a hydrophobic active substance.