Guns, hundreds of rounds of ammunition and a hunting knife are found in a car after convention center security tips off police.
The security team at the Hynes Convention Center had alerted authorities after threats were made over social media against attendees at the event.
The men – 18-year-old Kevin Norton, of Ames, and 27-year-old James Stumbo, of Boone – were stopped as they tried to enter the centre hours later.
Police released the men, but seized their car after learning there could be weapons inside.
After obtaining a search warrant, officers found a 12-gauge shotgun, an AR-15 rifle, several hundred rounds of ammunition and a hunting knife inside.
The men were then located and re-arrested at their hotel in Saugus, north of Boston.
They were arraigned at Boston Municipal Court on charges of unlawful possession of a firearm, unlawful possession of ammunition and other firearms charges.
Superintendent Paul Fitzgerald, Boston Police Department Intelligence and Analysis commander, praised the venue’s security team for contacting police about the “very real threat”.
In a statement, the Pokemon Company said it had been made aware of the threats by gamers attending the competition.
It said: “Prior to the event this weekend, our community of players made us aware of a security issue.
“We gathered information and gave it as soon as possible to the authorities at the John B Hynes Veterans Memorial Convention Center who acted swiftly and spearheaded communication with the Boston Police Department.
“Due to quick action, the potential threat was resolved. The Pokemon Company International takes the safety of our fans seriously and will continue to ensure proper security measures are a priority.”
Some 700 competitors took part in the event, which saw players battling each other in the Pokemon video game and trading card game. Hundreds more people attended as spectators or to take part in side events.
The championship, which ran from Friday to Sunday, is invitation-only with players competing for more than $500,000 in scholarship awards.