The investigation by the EHRC questioned 2,500 people about the laws protecting freedom of religion or belief.
It discovered widespread confusion over the legislation and many Christians reported that they feared their religion is losing its place in the workplace and in society more generally.
"A recurring theme among some employees was the pressure they felt they were under to keep their religion hidden at work and feeling discriminated against when it came to wearing religious symbols or expressing their beliefs," the report found.
It added: "People reported being mocked for their beliefs including Christians, who said their colleagues assumed they were bigoted."
The survey also discovered that some Christians claim they were excluded from meetings, or passed over for promotion or recruitment due to their faith and felt unable to raise the issue for fear of repercussions.
Some parents reported that their children were ridiculed in schools for their belief that God created the world.
But in the same survey a humanist parent reported that their child was told they didn't deserve Christmas presents because they didn't believe in God.
Some Christian-run services or businesses said they felt 'in turmoil' about behaving in ways that they feared might breach the Equality Act 2010.
Others argued they had lost public funding because of the faith element of their organisation.
The Evangelical Alliance welcomed the report and said it was a sign the EHRC was taking religious persecution in the UK seriously.
Dr Don Horrocks, head of public affairs at the EA, said: "We warmly welcome the new constructive tone from the Commission and that they finally seem to be trying to take religion and belief seriously and focus on properly recognising the protected characteristic of religion and belief.
"This comes after many years of largely ignoring Christians and actually opposing their concerns in the courts.
"However, there remains a clear reluctance to tackle infringement of freedom of conscience and the emergent hierarchy of human rights, which has left people of faith firmly at the bottom and often wondering whether in practice religion and belief is a protected right at all.
"There is a long way to go to achieve parity and equality on a fair playing field with other rights."
"When rights conflict, the test of equality legislation is whether it results in genuinely fair outcomes for everyone.
"If one group of protected rights is consistently trumped by others then equality is not working.
"Equality is important, but unless it is expressed fairly in the context of recognised diversity then it can become oppressive and end up being wielded as a blunt weapon to silence those we disagree with."
Mark Hammond, CEO of the Equality and Human Rights Commission, said: "How the law deals with religion and other beliefs in work, in providing services and in public debate has become a matter of considerable controversy.
"We carried out this consultation to gather first-hand evidence of how people deal with this issue in the workplace and in service delivery.
"What we found from the thousands of responses we received was a complex picture of different opinions and experiences.
"However, what came out strongly was the widespread confusion about the law, leading to some resentment and tensions between groups and anxiety for employers who fear falling foul of what they see as complicated equality and human rights legislation.
"We also found examples of organisations which had taken a constructive approach to dealing with issues of religion or belief, with employees providing positive experiences of diverse and inclusive workplaces.
"We'll use this evidence as we examine how effective the law is in this area and develop guidance which we hope will help everyone address some of the issues which have come out of the consultation."