Reverend David Court, 51, and Reverend David Randall, 42, both parted with the Church of Scotland after its General Assembly voted in May to affirm the Kirk's historic position on homosexuality while allowing congregations to elect ministers in civil partnerships if they wish.
Mr Randall follows in the footsteps of his brother Andrew and father David in taking the decision to leave the Kirk.
During his time in the Church of Scotland, Mr Randall pastored the Loudoun Newmilns congregation in Ayrshire and Bo'ness Old Kirk.
Mr Court was convener of CrossReach, the Church of Scotland's social care arm, for four years and had ministered to New Restalrig in Edinburgh and Balshagray Victoria Park in Glasgow since his ordination to the ministry in 1989.
He is current chair of Reformission Scotland, a charitable trust with the aim of encouraging the planting of new reformed, missional, Presbyterian churches in Scotland.
Both men are now available for a call to vacant congregations.
Mr Court said: "I am excited to be joining the Free Church of Scotland, a denomination that is known to honour the Scriptures, to love the Lord Jesus Christ, and to have a passion for the work of the gospel here in Scotland."
Mr Randall added: "I'm excited to be coming into a denomination that takes the Bible seriously and seeks to engage that biblical message with 21st century Scotland.
"What Scotland needs most today is the real Gospel of Jesus Christ, presented faithfully in engaging ways, and it seems to me that the Free Church is well placed to do exactly that.
"I'm grateful to the Free Church for the warmth of the welcome extended to me and look forward, under God, to the next stage of ministry that lies ahead."
A Free Church spokesman said: "It is clear from last week's census figures that many people go about their everyday lives without any thought of God or spiritual things.
"The need for preaching and sharing the Gospel is so great in Scotland today, and we believe Rev David Court and Rev David Randall will be important assets in communicating God's word in a changing environment over the years to come.
"Mr Court has a passion for church planting and to reach people who ordinarily wouldn't cross a church door on a Sunday.
"Having grown up under years of solid Bible teaching from his father, Mr Randall is one of Scotland's most gifted preachers and we look forward to supporting him in his ministry."