目前並無任何藥物治療和手術能根治克隆氏症。治療選項(英语:Management of Crohn's disease)的目的在於改善症狀,使病情緩解以及預防復發(英语:Relapse)。新診斷為克隆氏症的病人通常會接受短暫的類固醇治療,使病情有顯著的改善,之後並合併滅殺除癌錠或硫嘌呤等藥物防止復發。對於有菸癮的病患來說,在治療過程中最重要的一部分就是戒菸。患有克隆氏症的病患中,每五位就有一位需要每年定期回醫院覆診,其中約有一半的病患在發病後十年左右需要接受手術治療。雖然手術並非必要的治療方式,但適用於膿瘍、某些情況下的腸阻塞以及癌症。同時也建議患者在發病的八年後,需要隔幾年接受大腸鏡,以檢查是否有罹患大腸癌[4]。
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