This came after a scintillating qualifying round in which the pair set a new world record of 3:19.946 to book their place in the gold medal race.
Unfortunately, their world record last just until the next race as the Great British team of Lora Fachie and Corinne Hall outdid the Irish duo.
It was the Britain v Ireland in the battle for gold and following a much better start, the British team secured the gold medal at the Izu velodrome.
The pair are better known for their road cycling talents so landing a track silver wasn’t in their “wildest dreams”.
"I'm in a bit of shock, it is absolutely amazing," Dunlevy said on RTÉ this morning.
"If someone said to me before that I would get a medal in the pursuit I would never have thought it in my wildest dreams. We were hoping to do a good ride and get a PB. To get that and a world record, I’m just speechless."
McCrystal said the pair left nothing to chance and believed they acquitted themselves with pride: "I think we did ourselves proud, we left nothing to chance, no stone was left unturned by our coach Neill [Delahaye] and Cycling Ireland. He made sure that we would get here in the best possible form.
"To get that performance, I just can't believe it. I’m so proud of Katie and I know she is proud of me – I am just so happy that we did this."
President of Ireland Michael D. Higgins was among those who congratulated the duo on their success.
“My warmest congratulations to Katie-George Dunlevy & Eve McCrystal who today won silver in the B 3000m Individual Pursuit, adding to their remarkable record when representing Team Ireland,” President Higgins said.
Martin Gordon and Eamon Byrne were also in action in the 1,000m sprint event at the velodrome and finished fifth overall, landing a personal best in the process. Every para cycling competitor so far has achieved a personal when taking to the track in Tokyo.