Noticed there wasnt a list of such here so have thrown this up.

Catholic Churches in Istanbul

Cathedral Saint Esprit
Cumhuriyet Caddesi.
205 Harbiye

Everyday 18:00
Sunday 09:00 10:15-11:15
(212) 248 0910

Nostra Signora Del Rosaria
Yogurtcu Zulfi Sokak. 15
Bebek
Sundays 10:30-11:30
(212) 263 6186

Notre Dame De' Assumption
Cem Sakak. 5
Moda-Kadikoy
Everyday 18:30 Sundays 11:30
(216) 336 0322

Notre Dame De Lourdes
Kazim Orbay Caddesi. 29
Bomonti
Sundays 10:30
(212) 240 4047

St. Pacific
Yeni Sokak. 21
Buyuk Ada
Sundays Summer 10:30 Winter 11:00
(216) 382 6980

St. Antoine
Istiklal Caddesi. 325
Beyoglu
Everyday 18:00 Sunday 10:00-11:00
(212) 244 0935

Saint George
Kart Cinar Sokak. 10
Karakoy
Sunday 10:00
(212) 244 1882

Saint Paul
Cumhuriyet Caddesi. Selbasi Sokak. 5
Harbiye-Taksim
Sunday 11:30
(212) 248 3691

Santa Maria Draperies
Istiklal Caddesi. 429
Beyoglu
Everyday 08:00 Friday Saturday 17:00
Sunday 09:00 11:30 17:00
(212) 244 0243

Saint Louis
Nuruziya Sokak .22
Beyoglu
Saturday 19:00 Sunday 11:00
(212) 244 1075

Saint Stefano's
Cumbus Sokak. 8
Yesilkoy
Saturday 18:00 Sunday 10:30
(212) 573 8294

Santa Maria
Azagli Sokak. 5
Buyukdere
Saturday-Sunday
(212) 242 1817

Protestant churches in Istanbul


German Protestant Church St. Helene
Emin Cami Sokak. 40
Aynali Cesme Beyoglu
Sunday 10:30
250 3040

Dutch Church
Istiklal Caddesi. 393
Beyoglu / Taksim
Inside the Consulate
Sunday 09:30-11:0
251 5030 (3 lines)

Anglican Church

Mesrutiyet Caddesi. 34
Beyoglu
Inside the British consulate grounds
Sunday 10:00
244 4228
251 5616

Synagogues in Istanbul


Neve Shalom Synagogue
Buyuk Hendek Caddesi. No 67
Sishane Karakoy
(212) 293 7566

Ahrida Synagogue
Kurkcu Cesme Caddesi. No 9
Balat
(212) 523 4729

Hemdat Israel Synagogue
Yeldegirmeni Izzettin Sokak. No 61
Kadikoy
(216) 336 5293

Jewish Synagogue
Istasyon Arkasi
Sirkeci
(212) 513 3043

Etz-Ahayim Synagogue
Muallim naci Sokak. No 40/41
Ortakoy
(212) 260 1896

Bet Yaakov Synagogue
Icadiye Caddesi. No 9
Kuzguncuk
(216) 343 1698

Yenikoy Synagogue
Koybasi Caddesi. No 242
Yenikoy
(212) 223 1531

Italian Synagogue
Sahsuvar Sair ZiyaYokusu
Karakoy
(212) 293 7784

Askenaz Synagogue
Yuksek Kaldirim
Karakoy
(212) 243 6909

Sisli Synagogue
Osmanbey Efe Sokak. No 4
Sisli
(212) 240 6599

Caddebostan Ibadethanesi
Tas Mektep Sokak. 13
Goztepe
(216) 356 5922

Haskoy Maalem Synagogue
Harap Cesme Sokak .20
Haskoy
(212) 253 7160

Hesed Leavram Synagogue
Pancur Sokak. 15
Buyukada
(216) 382 5788

Burgazada Ibadethanesi
Koykahyasi Sokak 2/1
Burgazada
(216) 351 8549

Beth Yaakov Synagogue
Orhan Sokak. 12/1
Heybeliada

Also add the Anglican one Christ Church (Crimean Memorial Church) in Beyoğlu:

Christ Church (Anglican)
Address: Serdari Ekrem Sok. 82 Tunel Beyoglu Tel: (0212) 251 56 16