The Christian politician, who announced last month that he would step down as leader of the Liberal Democrats, said the counter-cultural nature of Christianity means resistance is inevitable.
Writing in the 'i' newspaper, he said: "Christianity is counter cultural and it always has been. In a society where self-fulfilment and personal autonomy are paramount, Christians believe that there is one God and that we are subject to him."
Mr Farron spoke after 93 per cent of people who took Premier's State of the Faith survey said they felt Christianity is being marginalised in society.
The MP, whose views on homosexuality drew intense scrutiny during the spring of this year, said he did not think he had personally been marginalised as a Christian in politics.
Mr Farron went on to suggest that the United Kingdom is probably the best country in the world in which to live freely as a Christian.
He added: "However, many Christians do feel marginalised, and they are meant to... the Bible tells us regularly that our faith will go against the grain, that we'll suffer for being a Christian. Being Christian is not meant to be easy."
Mr Farron said most people don't mind faith expressed in "funky garb" and "nice colourful festivals" but "the moment you show any signs of actually believing in this creed, of thinking that this stuff about Jesus might even be true or that this faith might in any way impact on your conscience or your life choices - well, we don't like that one bit."
Nearly 12,000 people took part in Premier's latest piece of research. Four in five said Christianity isn't given the same respect as other faiths and half reported having personally experienced prejudice against their faith.
The full results can be found at www.ordinarychristian.org.uk