ConEmu's startup option

Looks like there is no built-in option for ConEmu autostart. But there is an easy workaround - add it to autostart manually:

  1. Win+R -> open Run menu
  2. Type shell:startup, press Enter
  3. Create shortcut to ConEmu in opened folder

Piggybacking off The Godfather's solution which is correct, I would also add a -min to the end of the shortcut path you make or else ConEmu pops up randomly on startup interrupting you.