For a Muslim who usually neglects prayers, and after his repentance he still misses Isha’ and Fajr prayers, he has to bear in mind the fact that Prayer is the cornerstone of religion. In this context, the Prophet, peace and blessings be upon him, said, “Prayer is the cornerstone of religion…” Prayer stands as the second pillar of Islam after testifying that there is no god but Allah and Muhammad is His final Messenger. The Prophet, peace and blessings be upon him, said, “Islam is built upon five pillars: testifying that there is no true god except Allah and that Muhammad is the Messenger of Allah, performing Prayer, paying the Zakah, making the pilgrimage to the Sacred House (Hajj), and fasting the month of Ramadan.” (Reported by Al-Bukhari)
Prayer has a certain time in which a Muslim should offer it. Allah says, “Worship at fixed hours hath been enjoined on the believers.” (An-Nisa’: 103)
Also, the Prophet, peace and blessings be upon him, warned against ignoring offering Prayers in their due times.
Given the above, if a Muslim missed some prayers out of negligence, but seriously and sincerely repented to Allah, he has to make up for the prayers he missed. Sincere repentance, however, is not simply saying, “Lord, forgive me”, “I ask forgiveness of Allah.” Sincere repentance involves experiencing within oneself a profound sense of guilt for having disobeyed Allah and for the terrible sin one has committed. Secondly, one should totally refrain from approaching that sin as well as from such associations and circumstances that may led him/her to it; thirdly, one must be resolved never to repeat the same in the future, and finally, one must also do whatever he/she can to wipe out the past sins by engaging in good works as much as possible.
Once the above procedures are followed, we can look forward to Allah’s forgiveness for He is certainly All-Merciful and All-Forgiving.
So, it is our first advice to our Muslim brother in this condition to try his best to make up for what he has missed of obligatory prayers. He may pray each prayer twice, one for the current prayer and another for making up what he missed of prayers. He may continue doing so until he become pretty sure that he has made up for what he missed of prayers.
He also needs to spare no efforts to prayer `Isha’ and Fajr, in addition to other prayers, on their due times. He should try to take necessary measures that would help him perform prayer in their times.
Haven said this, as a Muslim we should never lose hope in gaining Allah’s mercy and forgiveness. Once we maintain sincere repentance, then be sure that Allah will forgive our sins. Allah says in the Qur’an: “Say: ‘O my Servants who have transgressed against their souls! Despair not of the Mercy of Allah: for Allah forgives all sins: for He is Oft-Forgiving, Most Merciful.'” (Az-Zumar: 53) and “Allah accepts the repentance of those who do evil in ignorance and repent soon afterwards; to them will Allah turn in mercy: For Allah is full of knowledge and wisdom.” (An-Nisa’: 17)
Also, The Prophet (peace and blessings be upon him)said, “Allah accepts the repentance of a person as long as death has not reached his collar bone (i.e., as long as it is not done in the last pangs of death).”