He apologized to the transgender student, however, Sutcliffe faces a disciplinary hearing this week and officials could charge him with misconduct for misgendering, the Evening Standard reported. "It was surreal, Kafkaesque", Sutcliffe said, according to the Daily Mail.
He said he did this by avoiding the use of gender-specific pronouns and by referring to the pupil by name.
"I was absolutely shocked to be told by the head that I was under investigation". I didn't know what was happening.
Sutcliffe admitted that, as a Christian, he was reticent to use male pronouns such as "he" and "him" and instead opted to use the student's name.
He believed this was consistent with the school's code of conduct and equality policies to show respect and tolerance, and he said he had encountered no problems with this.
The family of the transgender student is saying that Sutcliffe was "picking" on their child and they would not have complained about "misgendering" had they not thought otherwise because they are supporters of "free speech", reports the Mail.
"I said it was only one incident for which I had apologized, but he insisted the investigation would go ahead".
However, he had been summoned for questioning twice, and he was sent a letter telling him to attend a formal disciplinary hearing this Wednesday, attended by the head and three governors. "I have never looked to impose my convictions on others", Sutcliffe told BBC News.
He said he had raised religious issues such as the anniversary of the Reformation in his general tutor group, in which he encourages older pupils to discuss topical issues in the news, but not during maths classes.
Sutcliffe said was shocked by the school's actions, and felt out of depth and "intimidated" by the probe and upcoming hearing.
Sutcliffe has previously come under fire for his biblical view of gender and sexuality; several years ago, a voluntary Bible club he started during lunchtime was shut down after he answered a student's question on marriage by saying the Bible described it as being between a man and a woman.
Math teacher Joshua Sutcliffe, 27, said, "Well done, girls", to two students at an Oxfordshire secondary school. Sutcliffe said this did not occur in any math classes.
"This is one of a large number of cases we are encountering where teachers are finding themselves silenced or punished if they refuse to fall in line with the current transgender fad", said Andrea Williams, chief executive of the Christian Legal Center, which has been supporting Sutcliffe.
The maths teacher, who is also a pastor at the Christ Revelation church in Oxford, said he tried to balance his beliefs with the need to treat the pupil sensitively.
Sutcliffe thinks referring to someone by their birth gender isn't wrong or unreasonable, according to the Daily Mail.
The former Conservative Party chairman Lord Tebbit said: 'It seems to me this is a mad world when someone is disciplined for stating a biological fact'.
The headteacher of the school said they could not comment due to ongoing disciplinary matters.