Drug delivery at the nano-scale is becoming an important topic in nano and regenerative medicine as it can offer a very localized therapy. Therefore, niosomes are one of the most important vehicles to release drug at the nanoscale. In this paper, we present a new automated microsystem for niosome generation on-demand. Used niosome were based on a mixture of cholesterol and dicetyl phosphate with chloroform. Three compact micropumps are connected to a microfluidic substrate in order to generate 100 nm noisome vesicles. Through this paper we also investigated the impact of using 150 μm pseudo-Y and cross shape microchannel on the diameter of vesicles. We have observed reliable results with Y-shaped microchannel, which was able to generate vesicles down to 91 nm. All the system is based on a low-cost fabrication process using dry photo resist.