Lincolnshire Police said officers were called to the scene on Fountain Lane at around 6.20pm on Thursday.
The force said the area has been cordoned off and they will be at the scene for the foreseeable future.
Police said the incident is being treated as murder.
At the scene late on Thursday night, a police car was stationed either side of an alleyway to cordon the area off to the public.
Two forensic officers in white suits could be seen working at the scene before leaving in the early hours of Friday morning.
A large object appeared to be covered in the middle of the alleyway, which was marked by small yellow signs.
The victim’s parents have been informed, and the force said their “thoughts are with them at this incredibly difficult time”.
“Her family will be supported by specialist trained officers,” a short statement added.
The Conservative MP for Boston and Skegness, Matt Warman, said he had been in contact with the policing minister to ensure national assistance is available to the murder investigation.
“Profoundly shocking news in Boston this evening,” Mr Warman he said.
“I have spoken to senior officers locally and am hugely grateful for all the emergency services’ work.
“I have also been in contact with policing minister Tom Pursglove to ensure that any national help that might be useful is made available as quickly as possible.”
