It is permissible to pray in a church if there are no images or statues in it. 

Al-Bukhaari included a chapter in his Saheeh which he entitled: Chapter on praying in a “chapel”. ‘Umar (may Allah be pleased with him) said: We will not enter your churches because of the images in them. Ibn ‘Abbaas would pray in a “chapel” except a “chapel” in which there were statues. Ibn Hajar (may Allah have mercy on him) said: Chapter on praying in “chapels”; a “chapel” is a place of worship for Christians. The author of al-Muhkam said: The “chapel” is the cell of the monk, or, it was said, the church of the Christians, and the latter is the reliable view. The ruling on “chapels” also applies to churches, synagogues, hermits’ cells, temples in which there are idols, fire temples and so on. End quote. 

If there are images or statues in it, the fuqaha’ differed concerning the ruling on praying there in that case. Some of them are of the view that it is haraam, but the majority are of the view that it is makrooh. The reason given by those who regard it as haraam is the general meaning of the evidence which indicates that statues and keeping them are haraam, because the presence of these images prevents the angels from entering that place. 

Al-Bukhaari (3225) and Muslim (2106) narrated from Abu Talhah that the Prophet (blessings and peace of Allah be upon him) said: “The angels do not enter a house in which there is a dog or an image.” 

Al-Tirmidhi (2806) and Abu Dawood (4158) narrated that Abu Hurayrah said: The Messenger of Allah (blessings and peace of Allah be upon him) said: “Jibreel came to me and said: ‘I was going to come to you yesterday and nothing prevented me from entering upon you in the house where you were except that at the door of the house there was a statue of a man, and in the house there was a curtain on which there were images, and in the house there was a dog. So give instructions that the head of the statue at the door should be cut off, so that it will look like a tree. And give instructions that the curtain should be cut up and made into two pillows that will be placed on the ground and stepped on. And issue instructions that the dog be put outside.’” So the Messenger of Allah (blessings and peace of Allah be upon him) did that. And the dog was a puppy belonging to al-Hasan or al-Husayn that was under a bed, and he gave instructions that it should be taken outside.

This hadeeth was classed as saheeh by al-Albaani in Saheeh al-Jaami‘, no. 68. 

Ibn Qudaamah (may Allah have mercy on him) said: There is nothing wrong with praying in a church that is clean. That was allowed by al-Hasan, ‘Umar ibn ‘Abd al-‘Azeez, al-Sha‘bi, al-Awzaa‘i, and Sa‘eed ibn ‘Abd al-‘Azeez. It was also narrated from ‘Umar and Abu Moosa. Ibn ‘Abbaas and Maalik regarded churches as makrooh because of the images. But we know that the Prophet (blessings and peace of Allah be upon him) prayed at the Ka‘bah when there were images in it. It is also included in the words of the Prophet (blessings and peace of Allah be upon him): “Wherever you are when the time for prayer comes, pray, for it [the earth] is a place of prayer.”

End quote from al-Mughni, 1/407 

Among those who were of the view that it is haraam to pray in a church if there are images in it was Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him). See: al-Fataawa al-Kubra, 2/59 

The prohibition on praying in churches does not mean that such a prayer is invalid; rather the prayer is valid although it involves sin, because the reason why praying in churches is not allowed does not have to do with the prayer; rather it is because of the images in those places, as stated above. So the reason for the prohibition is different from the prayer and other matters pertaining to it. 

The Standing Committee and Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) issued fatwas stating that it is makrooh to pray in a place in which there are images, but the prayer is valid if that takes place. 

In Fataawa al-Lajnah al-Daa’imah (5/377) [vol. 2] it says: What is the ruling on praying in the house or room in which there are statues of animals or humans for decoration? 

Answer: It is haraam to keep images or statues and put them in houses, because the Prophet (blessings and peace of Allah be upon him) said to ‘Ali (may Allah be pleased with him): “Do not leave any image without erasing it or any built-up grave without levelling it.” And because he (blessings and peace of Allah be upon him) said: “The angels do not enter a house in which there is a dog or an image.” It is makrooh to pray in a room in which there are pictures hanging or statues, especially if they are in front of the person when he faces the qiblah. But the prayer is valid. 

And Allah is the source of strength. May Allah send blessings and peace upon our Prophet Muhammad and his family and Companions. 

Standing Committee for Academic Research and Issuing Fatwas. 

Bakr Abu Zayd, ‘Abd al-‘Azeez Aal al-Shaykh, Saalih al-Fawzaan, ‘Abd-Allah ibn Ghadyaan, ‘Abd al-Razzaaq ‘Afeefi, ‘Abd al-‘Azeez ibn ‘Abd-Allah ibn Baaz. End quote. 

Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) said:… As for the prayer, it is valid, but it is makrooh to pray in a place in which there are images except in the case of necessity; if nothing else is available, then there is nothing wrong with it. End quote. 

To sum up: 

1.There is nothing wrong with praying inside the church if it is free of images and statues, whether that is Jumu‘ah prayer or any other prayer.

2.It is makrooh to pray in a church if there are images or statues in it. If the Muslims need to pray there because there is no other place available, and they cover these statues with something that will conceal them, there is nothing wrong with it and it is not makrooh.

And Allah knows best.