Around 70 others were injured at the Reina club in the city's Ortakoy neighbourhood.
The gunman responsible still hasn't been caught but is reported to be part of an Islamic State cell.
It was the fourth terrorist attack in Turkey in less than a month.
WCC general secretary, Rev Dr Olav Fykse Tveit said: "Yet, another terror attack in Istanbul. Innocent people are suffering again and again.
"This is an evil act. This attack is particularly shocking, in the first place because there seems to have been a clear intention deliberately to target people who were simply enjoying themselves at the New Year's Day.
"In the face of this brutality, the human family, all people of faith and of good will, must stand together to recommit to respecting and caring for one another, to protecting one another, and to preventing such violence."
Meanwhile Theresa May has written to Turkey's president to offer support following the attack.
She's underlined the UK's commitment to defeating terrorism.