Why is there a setup fee?
It covers the underwriting work on your file and, in categories requiring card scheme registration, real fees the acquirer has to pay. It is worth asking what it is for, because the answer distinguishes a cost from a margin.
Setup fees in high risk usually run from $250 to $1,500, and they cover two quite different things that are worth separating when you ask.
Real external costs. Some categories require registration with the card schemes before you can process. Those registration fees are genuinely paid out by the acquirer, they are often annual, and they are not negotiable by anyone in the chain.
Underwriting effort. Reviewing a complex file takes an underwriter’s time, and a high-risk file takes more of it. This portion is a commercial charge and behaves like one.
The useful question is therefore not “can you waive the setup fee” but “how much of this is scheme registration”. A provider who can answer that precisely is telling you something about how they operate. A provider who cannot, or who quotes a round number with no breakdown, is telling you something too.
Be wary of a setup fee charged before any underwriting has happened. Paying to be assessed is different from paying to be boarded, and the first arrangement gives the provider no reason to be honest with you about your chances.