The burglary happened shortly after 2:00 a.m. Sunday at Benchmark Transmission at 2610 Philadelphia Pike.
Police were called after someone noticed something suspicious outside the shop.
Once they arrived, officers say they found 21-year-old Sylvester Rogers of Chester, 20-year-old Victor Peeples of Marcus Hook and a 16-year-old Claymont boy inside a car.
Investigators say the three broke into the business through a window and removed nine sets of keys. One set of keys belonged to the vehicle in which the men were sitting, police say.
All three were charged with burglary and theft and ordered to be held on $4,100 secured bail.