The security breach came the day before Fulham played Tottenham in the Premier League last Thursday.
Suspicions were raised over the presence of the two men inside the ground and police were called after Fulham reviewed CCTV footage.
There were initially concerns that the incident may have been terror-related.
The motive of the men is unclear but Premier League clubs are on alert amid fears that an organised crime gang could be targeting top-flight stadiums, either as part of a gambling scam or an extortion attempt to capture something said by broadcast teams.
A Met spokesperson said: “We received a report of an alleged security breach at Fulham stadium, where two men gained entry.
“The incident is reported to have happened on Wednesday, March 3. The circumstances of this report are being examined to see if any criminal offences were committed. There have been no arrests and enquiries continue.”
A spokesman for Fulham confirmed they are assisting police.