The mobile has left the United Kingdom and is expected to arrive the West African country by middle of July.
Arsenal first-team squad are expected in Nigeria this summer for a pre-season match on Sunday, August 5.
According to David Omigie of DanJan sports, an agreement has been reached alongside Arsenal with Vanguard Healthcare, the world's largest fleet of mobile healthcare facilities.
The theatre is required during Arsenal's close season trip.
Omigie: "This mobile operating theatre is not only essential for the players but the fans as well."
"Considering the last incident with Fabrice Muamba, the lives of players, officials, fans and everyone involved is of great importance. Safety is paramount.
"In case of an emergency it can easily accommodate more than fifteen people, so we are happy to have finalised everything on time."
Meanwhile, SIFAX shipping company are the chosen importation agent for Danjan sports on this tour.
Omigie revealed that SIFAX were chosen for their expertise and professionalism of getting units like this cleared quickly by customs.
"We are happy to announce that SIFAX have been proven reliable and trusted."