The Christian Association of Nigeria (CAN) says the attacks amount to genocide but authorities are "turning a blind eye" to the violence.
It says armed Fulani herdsmen are carrying out widespread attacks in Christian villages in the north.
It says they will often fire shots into the air at night then kill villagers as they run from their homes in fear.
The day of mourning is being supported by religious freedom group Release International.
Chief Executive Paul Robinson said: "Christians in the north are facing the twin terrors of Boko Haram and this largely unreported widespread menace of heavily-armed Fulani.
"Both groups are bent on killing Christians and cleansing the north of its Christian minority.
"Nigeria has become a country of special concern to Release. Thousands are dying and Release shares the dismay of Christian leaders in Nigeria at the apparent inaction and indifference by the government and its security forces. We add our support to the Christian Association of Nigeria."
The Christian Association of Nigeria is calling on all Nigerians to wear black on 8th January in solidarity with the thousands who have died and have been driven from their homes.
In a statement, CAN President Rev Dr Samson Olasupo Ayokunle said: "The church in Nigeria since 2009 has been subjected to a systemic genocide and persecution [by] Islamic fundamentalists...leading to the killing of thousands of Christians and destruction of hundreds of churches, and over 50,000 houses."
The call comes days after the Anglican Archbishop of Jos, the Rt Rev Benjamin Kwashi, warned that there could be a civil war between Christians and Muslims if Christians seek revenge.
Whilst not advocating for revenge, the Archbishop said believers are angry and feel as if no one is protecting them.
Listen to Andrew Boyd from Release International speaking to Premier's Marcus Jones.