It was ruling on a case in Hungary in which a pastor was sacked by his church.
In 2005, Karoly Nagy was removed from his post by an ecclesiastical court. He later appealed but was dismissed.
He then took the case to the Hungarian Supreme Court which said it had no right to overrule the church's legal system.
Mr Nagy asked the ECHR to force the state courts to intervene. However the ECHR ruled against him.
The case heard evidence from the religious freedom charity ADF International which argued the state has no place interfering in the relationship between a church and its leaders.
Welcoming the ruling, Paul Coleman (pictured above), Deputy Director of ADF International, said: "ADF International intervened in this case to highlight the principle of church autonomy in handling internal disciplinary matters.
"International law and especially the European Convention on Human Rights protects this fundamental freedom. The state shall have no role in meddling with the internal governance of religious institutions.
"This Grand Chamber judgment has confirmed the principle of church autonomy by dismissing a claim by a former pastor that he was entitled to use the state courts against a church when he was unhappy with the decisions of the internal ecclesiastical courts.
"This decision is welcome as it reinforces the rights of religious believers in all 47 member states of the Council of Europe to manage their own affairs without unwarranted external interference."