Question:
I ask about Du’a in hard times. There are some Ahadeeth in Saheeh Muslim which mentions that the Qunoot is Sunnah? Do we have to do it for every prayer?
Fatwa:
All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
As a rule, Qunoot (supplication) is a Sunnah (tradition) of Prophet 
. According to the opinion of Imam Ahmad and Imam Abu Hanefah 
Qunoot is a Sunnah in Al-Witr prayer. It is better to make Qunoot in Al-Witr prayer before Rukoo’, although it is acceptable to be after Rukoo’.
However, if any disaster or calamity befalls Muslims, such as epidemics, floods, fear from the enemy’s outrage, aggression, oppression or injustice, they are ordained to supplicate in Qunoot in the last Rak’ah of every obligatory prayer. Qunoot should be before or after the Rukoo’.
Here are some evidence regarding Qunoot:
1. It is narrated by Ahmad, Muslim, An-Nasa’i and Ibn Majah on the authority of Anas that the Prophet Muhammad supplicated Qunoot for one whole month, calling down the wrath of Allah upon some Arab tribes (Arabs from Banu Sulaim, Rei’l and Thakwaan), then he left it (didn’t supplicate Qunoot anymore). Al-Bukhari’s narration (reads); “He (the Prophet Muhammad ) supplicated with Qunoot when his missionaries (Qurra’) were killed (by Arab tribes, Banu Sulaim, Rei’l and Thakwaan). I didn’t see him more grieved of any incident as he was in this incident.”
2. It is narrated by Ahmad, Muslim and at-Tirmithi on the authority of Al-Bara’ Ibn ‘Aazeb that the Prophet Muhammad supplicated with Qunoot in Maghrib and Fajr prayers.
3. It is narrated by Ahmad and Abu Dawood on the authority of Ibn Abbas who said: “The Prophet supplicated with Qunoot continuously during a whole month in Thuhr, Asr, Maghrib, ‘Ishaa, and Subh (Fajr) in the end of the prayer. He (the Prophet Muhammad ) recited (Qunoot) after raising from Rukoo’ in the last Rak’ah, and then he called down the wrath of Allah upon Banu Sulaim, Rei’l, Thakwaan and ‘Osayyah, and the followers (his companions who were praying after him) were saying Ameen.“
4. Qunoot should be preformed in the last Rak’ah of Thuhr and ‘Ishaa prayer, and in the Fajr prayer after saying: ‘Sami Allahu Liman Hamidah’ (Allah hears the one who praises Him). The supplicant should pray for believers and invoke evil on infidels.
As for Qunoot daily in Fajr prayer, there is a disagreement among Muslim scholars concerning this issue. Imams Ahmad and Abu Haneefah held the opinion that it is not a Sunnah to make Qunoot in Fajr prayer or any other prayer except Al-Witr. Malik Al-Ashjai’e said to his father Abu Malik Al-Ashjai’e : ‘You prayed with Allah’s Messenger , Abu Bakr, ‘Umar, Uthman and with ‘Ali here in Kufa for five years. Did they make Qunoot in al-Fajr?’ His father replied: ‘O my son! It is something that has been innovated.’ (Reported by At-Tirmithi). Most scholars follow such a rule. However, Imams Malik and al-Shafi’e held the opinion that it is a Sunnah to make Qunoot in Fajr prayer at all times.
Allaah Knows best.
Fatwa answered by: The Fatwa Center at Islamweb