If you make a refugee claim, a removal order is made against you which becomes a deportation order if your case ends unsuccessfully and you do not leave within a specified period of time.
If you lost your refugee claim at the Refugee Protection Division (RPD), and appealed to the Refugee Appeal Division (RAD), then the removal order will come into force, but be “stayed” (put on hold) while you are applying to the Federal Court. This stay of removal is automatic (as long as you apply to the Federal Court on time, and don’t fall under a handful of exceptions) under s. 231 of the Immigration Regulations. You will continue to benefit from most of the conditions from which you benefited when your case was before the RPD and RAD (health care, access to a work permit, ability for children to attend school), although the processes for applying may be different, you may need to pay processing fees, and you may be granted shorter permits.
If the automatic stay does not apply to you, you can ask the Court to stay (put on hold) your removal while your case is ongoing.