The action over pay, which is taking place between 7am on Thursday, 6 June and 7am on Thursday, 8, follows news that junior doctors in England will walk out between 27 June and 2 July.
Dr Fiona Griffin, chair of BMA's Northern Ireland junior doctors committee, said: ‘The new health minister needs to seize the opportunity of solving this dispute once and for all by putting forward a credible offer that includes meaningful steps towards full pay restoration.
‘We do not want to have to call further strikes but we will be left with no choice but to do so if there is no movement on pay.'
Junior doctors in Northern Ireland held their first strike on 6 March.
The BMA said their pay has been eroded by over 30% since 2008.
A Department of Health spokesperson said: ‘When the ballot for this industrial action was launched, junior doctors, like the rest of Northern Ireland's health service staff, had received no pay award for 2023/24.
‘This is no longer the case. A backdated 2023/24 pay award for junior doctors will be paid this month, with its terms in line with the recommendations of the national pay review body, the DDRB.
‘This pay award involves an average pay increase of 9.07% for junior doctors in Northern Ireland, with those in their first year receiving a 10.68% uplift.'