You have three non-exclusive options, each carrying its own advantages and disadvantages

Agency Level Protest:

You can submit your protest to the contracting officer, the very person who’s actions you are protesting.

An Agency Protest is generally inexpensive, quick (usually resolved in 30 days) and often does not involve a lawyer (because most experienced bid protest lawyers advise against Agency protests).

Agency protests are very rarely successful.  They are advisable only for gross and obvious agency errors or to send a message to the contracting officer.

Loss of an agency protest can be appealed to the GAO, but some of the advantages of a GAO protest are lost if you protest to the Agency first.
 

GAO Protest:

You can submit your protest directly to the Government Accountability Office (GAO).

This is a relatively inexpensive venue, but is more likely to succeed if you have a lawyer. Recent GAO statistics show the likelihood of achieving some success is about 45% (“effectiveness rate”).

It can be procedurally challenging because of very short deadlines for filing and complex rules for disclosure of information, but not as complicated as a federal court filing.

By law, GAO protests are resolved within 100 days of filing the protest.

Court of Federal Claims Protest:

You can submit your protest directly to the U.S. Court of Federal Claims.  Like any federal court litigation, this can be very expensive, requires an attorney, and requires that the U.S. Department of Justice defend the Agency in court.

Because of its more relaxed time deadlines, sometimes it’s the only option if you are too late to file at GAO.  Judges have more power and flexibility in assessing your allegations and providing a remedy.

Sometimes a Court of Federal Claims protest is resolved in eight to ten weeks, but it can take much longer.