Canon Stephen Palmer, 68, assaulted the girl at his home while he was a curate and youth worker in Stubbington, Hampshire, between 1975 and 1976.
A husband and father of two, his wife was out at the time taking their children to school.
He was named an honorary chaplain to Queen Elizabeth II in 2008.
A jury found him guilty of six counts of indecent assault, with the judge sentencing Mr Palmer to three years and three months in prison.
The victim, now an adult, told Portsmouth Crown Court: "You think of people in the church as caring and trustworthy, but this was not my experience.
"I couldn't cope with what happened."
A spokesman for the Diocese of Portsmouth said: "We were distressed to hear that a former vicar from this diocese, the Rev Stephen Palmer, had been convicted on charges of indecent assault.
"Our thoughts and prayers are with the victim, who has had to live with the consequences of these assaults for many years.
"Since the 1970s, safeguarding procedures and policies have been transformed in the Church of England, as well as in society generally. The safety of the children and young people in our care is paramount.
"Each of our parishes is required to follow detailed safeguarding policies to ensure that our children and young people are kept safe."
