The payment system represents a sum of instruments, procedures and infrastructure for money transfer. It is of great importance for all economic agents since it enables fast and efficient payments in the national economy as well as internationally. Electronic payment system functionality is measured through analysis of the transactions committed, structure of the electronic instruments available within a country, and payment instruments used during payment of purchased or ordered products or services. The use of Electronic Payment Instruments in Macedonia is growing steadily, which shows that the EPS system in this country is continually growing and is in some extend well organized, people are friendly to ICT and conduct electronic transactions easily. E-banking activities in Macedonia started, but remain in low levels; which is a fact for e-commerce activities in general.