There are no natural remedies for pilonidal cysts. A pilonidal cyst, if infected, requires surgical excision and cleaning. Without this procedure it can become infected and cause serious complications.
The best thing I have found for a pilonidal cyst is regular exercise. Walking on a treadmill or using an elliptical machine are two options that work well.
The best remedy for a pilonidal cyst is to have it incised and drained. Healing works best by leaving it open with packing. The packing can be removed slowly.