The warning includes central Cook Count, DuPage County, northeastern Kendall County, northwestern Will County and southeastern Kane County until 2 a.m. Monday.
National weather service Doppler radar indicated slow moving thunderstorms with very heavy rainfall across the warned area.
There are reports of several inches of water accumulating on Route 34 in Naperville.
Doppler radar estimates that between one and two inches of rain has fallen across the warned area over the past hour.
Additional rainfall of one to two inches is expected before the rainfall begins to taper off later Sunday evening.
Runoff from this excessive rainfall will cause flash flooding to occur. Some locations that will experience flooding include Addison, Aurora. Naperville, Batavia, Bolingbrook, Burr Ridge, Carol Stream, Downers Grove, DuPage Airport, Elmhurst, Geneva, Glen Ellyn, Hinsdale, Lemont, Lisle and Lombard.