Bootloader-less Programming Arduino Pro Mini

Recently I was creating a configurable timer circuit based Arduino Pro Mini. The circuit has a momentary push button which user can press to turn ON the device. The device will turn OFF itself once the time is elapsed. On starting, Arduino has to turn on a relay to get permanent connection to power source, so it will get power when user released the push button. One issue I faced was that Arduino takes around 3 seconds to start executing the program because of the presence of the bootloader.