All perfect praise be to Allaah, The Lord of the worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and Messenger.
Whoever delays the ‘Ishaa' prayer deliberately until its due times elapses has committed a manifest sin and should repent to Allaah The Exalted for it and observe the obligatory prayers in their due times. Allaah The Exalted Says (what means): {Maintain with care the [obligatory] prayers and [in particular] the middle prayer and stand before Allaah, devoutly obedient.}[Quran 2:238]
Most scholars believe that a Muslim is obliged to make up for a missed prayer, which he had neglected deliberately, and this is more prudent and safer in terms of clearing liability. However, there is no relation between the performance of the ‘Ishaa' prayer and the validity or acceptance of the Fajr prayer. This means that, missing the ‘Ishaa’ prayer will not render the Fajr prayer unacceptable and this is the case with all the obligatory prayers.
In such a case, one should make up for the missed ‘Ishaa' prayer first before performing the Fajr prayer. This is because observing proper sequence between a missed prayer and the current one while making up for it is obligatory according to the preponderant opinion of scholars. Nevertheless, if there was not enough time before the end time of the current prayer, one may perform it first and then make up for the missed one afterwards.