The Archdiocese of Birmingham has acted on advice that lessons covering sexuality should begin earlier in children's development.
Official figures show that the city has a high rate of teenage pregnancies.
Senior Catholic figures behind the pound;25,000 project, funded with government money, believe the Church must recognise young people's earlier sexual awareness and the pressures they face.
Father Joseph Quigley, director of religious education for the diocese, said: "We know what children are experiencing on television and in magazines, which means their maturation is taking place earlier.
"We don't want to leave children hostage to society. If we talk about sexuality as a gift, clearly we want to introduce them to that at an appropriate level."
The new sex and relationship education system, entitled All that I am, includes a teaching programme for primary schools and a video.
Church officials spoke to 50 Catholic 14 and 15-year-olds in Birmingham about their experiences of sex education to produce the programme, which took 18 months to complete.
The teaching programme includes discussions on menstruation, how to manage awkward situations and the meaning of friendships.
Catholic parents will still have the right to withdraw their children from sex education, while a new programme aimed at older children will not include details of contraception.
Previously, sex education in Catholic schools was introduced in Year 6 for 10 and 11-year-olds in science lessons. Traditionally, the Church has believed the main responsibility for it lies with parents.
The Roman Catholic Church decided to introduce sex education at Year 5, to nine and 10-year-olds, after working with Birmingham council's health education unit.
The move brings the city's Catholic schools into line with their council counterparts, where sex education is also introduced from the age of nine.
Father Quigley said: "I'm convinced that trying to lower the teenage pregnancy rate is intimately related to trying to improve young people's self- esteem and understanding of their dignity.
"Children are told they are made in the image and light of God. But they don't understand what that means.
"What we are trying to do is allow children to understand their personal development and also appreciate the Church's teachings."
"If we reduce the ways of looking at development simply to strategies for saying 'no', we are failing to understand the issue of dignity and the gift of sexuality."