Blackpool Transport, which oversees the buses, claimed the ads "resulted in heightened tension".
A number of people had taken to social media to claim that Franklin Graham would be preaching hate and homophobia at the event which is due to take place at the city's Winter Gardens in September.
Jane Cole, Managing Director at Blackpool Transport said: "The removal of these adverts is as a result of us listening and acting on customer and public feedback which we aim to do at all times.
"Blackpool Transport is a proud ongoing supporter of the Pride and LGBT+ communities and in no way did we intend to cause any distress or upset."
A number of MPs have raised concern about his visit to Blackpool fearing he will repeat previous statements condemning homosexuality and Islam.
But speaking to Premier earlier this year, Graham said: "I'm not coming to preach hate, I'm here to preach about a saviour - Jesus Christ who can make a difference in our lives if we put our faith and trust in him."
His visit is however is being supported by many local church leaders.
Franklin Graham has led evangelism events across the world in his role as president of the Billy Graham Evangelistic Association.
He's also reached millions of people through his aid work with the charity Samaritans Purse.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.