Firefighters from Bracknell, Wokingham and Windsor were called to the incident at Lloyds Pharmacy portable cabin next to the former 3M building at about 2am.
Crews spent about two hours at the Market Street pharmacy after police had alerted them.
Four firefighters used breathing apparatus while crews also used two hose reels and two hydrants to battle the flames.
Bracknell's crew manager Richie Sage said they believed someone had set fire to items outside before the pharmacy became engulfed by the flames.
He said: "Most of the damage was to the storage area at the bottom half of the pharmacy. The actual contents of the shop were fine."
Police also confirmed they were still on the scene investigating the cause of the blaze.