David Black was murdered as he drove to work on Thursday
Mr Black, 52, was attacked on the M1 motorway in County Armagh as he drove to work on Thursday.
A car drove up beside his vehicle and fired a number of shots. His car veered into a ditch and he died at the scene.
Both of the arrested men have been taken to Antrim police station for questioning.
Mr Black, a father-of-two from Cookstown in County Tyrone, was the first prison officer to be murdered in Northern Ireland in almost 20 years.
The Police Service of Northern Ireland (PSNI) have said they believe dissident republican paramilitaries were responsible for the attack.
The murder has been condemned by all political parties in Northern Ireland.
Mr Black was driving towards Maghaberry Prison when he was shot on a stretch of the motorway between Portadown and Lurgan at 07:30 GMT on Thursday.
A car with Dublin registration plates, which is believed to have been used in the attack, was later found burned out at Inglewood in Lurgan.
PSNI Assistant Chief Constable Drew Harris said Mr Black had sustained very serious and probably fatal gunshot wounds.
He was a very experienced prison officer and had worked with the service throughout the Troubles.
He was the 30th prison worker to be murdered by paramilitaries since 1974 in Northern Ireland.
A book of condolence is due to be opened in Mr Black’s home town on Friday afternoon.
A spokeswoman for Cookstown District Council said the book would be opened to the public at Burnavon Arts and Culture Centre on Burn Road in Cookstown at 12:00 GMT.
The Secretary of State for Northern Ireland, Theresa Villiers, is due to make a statement on the killing in the House of Commons on Friday morning.
WITH MANY THANKS TO : BBC NEWS.
- Ministers to discuss M1 murder (bbc.co.uk)
- Two men arrested following the motorway murder of prison officer (independent.ie)
- Two men arrested over Northern Ireland prison officer murder (guardian.co.uk)
- Duffy Arrested Over NI Prison Officer Murder (sfluxe.com)