The demonstration forced Unai Emery’s men to travel to the third division club’s Bloomfield Road ground in another bus.
Since being in the Premier League in 2010, Blackpool slipped to the fourth division, before promotion to the third tier in 2017.
Fans protested against the club’s owners, the Oyston family, outside the stadium ahead of Saturday’s high-profile third round clash.
The bus protester was eventually talked down before being arrested.
There were rows of empty seats inside the ground with more than 5,000 of the 9,000 fans supporting Arsenal.
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