The item was discovered in Kenwyne Jones' locker at the club's training ground, although manager Tony Pulis admits he was unaware of the incident
Stoke midfielder Brek Shea posted an image of the pig's head on Twitter with the caption: "Locker room banter gone wild!!!".
"The club takes seriously reports of an incident at our training ground this afternoon," read a statement on the club's official website.
"A full internal investigation will be carried out and those responsible for any unacceptable behaviour will be dealt with in accordance with the club’s disciplinary procedures."
Stoke manager Tony Pulis admits he was unaware of the incident but claims he will speak to his squad regarding the incident prior to the club's final game of the season against Southampton on Sunday.
"We have a smashing dressing room, and there are four or five lads who are always up to something. There is always banter going on," Pulis told BBC Radio Five Live.
"I honestly don't know what's gone on this morning, I've missed all of what's happened. I try to stay away from the home dressing room as much as I possibly can, I let the lads get on with it.
"We will look at it tomorrow, I will have a chat with the lads and find out exactly what has happened.
"From that point onwards we'll let everybody know exactly what the situation was."