If a pilonidal cyst becomes acutely infected, it is now called a Pilonidal Abscess. The symptoms of this are severe discomfort; a red, tender lump; and possibly a fever. The natural course of these abscesses can very: it might drain on its own and subside, or it might not drain and require surgical drainage.
If you are experiencing this, the best option is to see a surgeon for diagnosis and treatment. If this is not something that you can do, it is possible to get this to drain with warm compresses to the area or soaking in a warm tub. The heat has a tendency to bring the abscess to a head so it can drain. Unfortunately, some of these infections are so deep that this never happens without surgical intervention. Antibiotics may be slightly helpful, but if an abscess really needs to be drained they will just postpone the inevitable. The longer a patient waits, the larger the abscess may become, and the longer the healing process once it is drained.