Local security officials said the attack occurred when people were performing Friday Prayers in the town of Shikarpur, around 470 kilometers (300 miles) north of the port city of Karachi.
Sindh Health Minister Jam Mehtab Daher told AFP that "a total of 40 have been killed in the attack, 46 others have been wounded".
A number of victims are still trapped under debris, after the roof of the mosque collapsed due to the intensive blast.
No group has yet claimed responsibility, but pro-Taliban militants usually take responsibility for similar attacks in the violence-wracked country.
This is also the latest deadly incident in a wave of violence against the Shia Muslim community in Pakistan.
Pro-Taliban and al-Qaeda-linked militants, who are reportedly behind the killings, have imposed an economic blockade against the Shia-dominated population areas across the volatile northwest.
The frequent incidents have raised concerns among human rights groups, while moderate Pakistani Sunni groups have described the issue as a conspiracy against the country.
Taliban leaders, who were toppled in the 2001 US-led invasion of Afghanistan, took refuge in tribal regions of Pakistan and rapidly began to extend their influence from tribes to major towns and cities.
Shia Muslims in Pakistan say the government must take decisive action against the forces involved in the targeted killings. They also accuse Islamabad of failing to provide security for the Muslim community.
The killing of Shias has caused international outrage, with rights groups and regional countries expressing concern over the ongoing deadly violence. Shias make up about a third of Pakistan’s population of over 180 million.
/149