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The Scottish Episcopal Church voted against electing Britain's first female bishop, despite the church voting to consecrate women in 2003.
A majority of an electoral synod of clergy and church members chose a more experienced male candidate over Reverend Alison Peden, 57, the first woman to be shortlisted to become a bishop since the 2003 vote.
The Courier Mail reports Peden was one of three candidates.
She lost out to Reverend Gregor Duncan, 59, who is already dean of Glasgow and Galloway - the diocese for which the election was being held.
Primus of the Scottish Episcopal Church, Bishop David Chillingworth, who chaired the electoral synod, said gender had not played a part in the decision and Peden being shortlisted had helped change the perception of women in the church.
"In any profession when women are admitted inevitably it takes a while for them to acquire the experience and to work their way through the ranks or the levels of authority," he told the BBC.
"What we are seeing now for the first time is women ... expecting and deserving to be taken seriously at this level and I'm sure it will come about before too long."
If Peden had been elected it would have increased pressure on the Church of England to follow suit.
The CoE, which is still struggling to accommodate both liberals who demand equality and traditionalists who want to keep the all-male senior clergy, is set to receive an update on the consecration of women at its General Synod, or parliament, next month.
