We demonstrate that polyelectrolyte (PE) multilayer thin films deposited on patterned posts with incredibly large numbers of bilayers, which would not be possible with the conventional Layer-by-Layer (LbL) deposition methods, can be obtained in a short process time using alternating polyelectrolyte droplets generated in a microfluidic channel, representing a significant advantage over the conventional processes based on polyelectrolyte deposition followed by the separation of such substrates (typically colloidal particles) with centrifugation and sonication. Positively- and negatively-charged polyelectrolyte droplets were alternatively generated in a microfluidic channel by controlling the capillary number (Ca) as well as the fraction of dispersed phase over the continuous phase. Patterned posts, serving as the substrates for the PE deposition, were created with photo-curable polymers using the optofluidic maskless lithography. The impact of these PE droplets onto the patterned posts allowed the alternative adsorption of PEs, similar to the conventional LbL deposition methods. It was shown that the intensity of fluorescence dye tagged onto (+)-charged PEs adsorbed on the post(s), taken with confocal laser scanning microscopy, increases with deposition time and varies around the post(s). The effect of post shape and interval between the two posts for the droplet-based LbL deposition was also experimentally investigated and analyzed, in connection with the numerical simulations, to elucidate the underlying principles of relevant two-phase flows.