Lens arrays are introduced to diminish the total internal reflection (TIR) that happens at chip-encapsulant and encapsulant-air interfaces of chip-on-board light-emitting diodes (COB-LEDs), so as to improve the light extraction efficiency (LEE) of the COB-LEDs. However, the LEE of COB-LEDs with lens array depends on the refractive index of the encapsulant layer nencap and lens array nlens, which was rarely concerned so far. Optical simulations based on a Monte Carlo ray tracing method, and experiments were conducted to investigate the effect of nencap and nlens on the LEE of COB-LEDs with millilens array. The simulated results show that the TIR at chip-encapsulant, encapsulant-lens, and lens-air interfaces can be significantly diminished by regulating the nencap and nlens, and the LEE of COB-LEDs decreases as the refractive difference of encapsulant layer and lens array |nlens-nencap| increases. Compared to the COB-LEDs with only a flat encapsulant layer, the LEEs of blue and white COB-LEDs with nlens=nencap=nITO=2 are enhanced by 246.2% and 50.6%, where nITO is the refractive index of the top layer of the conventional LED chip. The experimental results agree well with the simulated results with normalized LEE deviation within 7.3%.