Andrew Foreshew-Cain raised the rainbow and transgender flags above his church, St James' in West Hamsptead, on Friday after vandals tore them down earlier this month.
He was helped by firefighters and watched by local politicians including the Hampstead and Kilburn MP Tulip Siddiq.
But the flags were again targeted on Saturday, and Fr Foreshew-Cain put them up even higher, using a stage ladder, after the morning service yesterday.
Asked why he felt the need to fly the flags, the vicar said: "We are a progressive and inclusive parish and we believe that God's love is for everybody."
He went on to criticise the Church's position. "The Church's current institutional homophobia needs to be challenged and that's what we're trying to do. It's like an abuser – apologise then hurt someone again. The Church's current stance and policies hurt LGBT people and it is a deliberate set of policies. All the apologies in the world are meaningless until the Church changes its behaviour. And by church I mean the bishops of the church."