The game kicked-off with queues still at the turnstiles and ticket offices.
North End do not take cash on the turnstiles, fans having to buy a ticket before entering the ground.
Tuesday night’s game attracted a larger than normal walk-up crowd with it being a cup game and not covered by season tickets – prices had been reduced to £10 for fans aged 17 and above, and £1 for those 16 and under.
Fans took to social media to vent their frustration at the long queues, some saying they had turned round and gone home rather than queue.
The attendance was 4,509, with 180 travelling from Hartlepool.
PNE issued a statement from chief executive John Kay in response to a request by the Evening Post.
Kay said: ”Preston North End are aware of the frustration regarding queuing for supporters at Deepdale ahead of the EFL Cup tie against Hartlepool United.
“We understand these frustrations, however, there are inevitably going to be long queues when large numbers of supporters arrive so close to kick-off to buy tickets.
“We do not operate cash turnstiles at Deepdale, all entry is by ticket and we are unable to delay the match start time; this remains the responsibility of the match officials.
“Tickets for home games at Deepdale are on sale for weeks in advance of the match and are available in person from the ticket office and over the phone during opening hours as well as the option to purchase online 24/7.
“Tickets can be collected from the collection window.
“Supporters are given the opportunity to purchase tickets well in advance and we urge fans to purchase ahead of the game to avoid queues like we saw on Tuesday night.
“We have operated the same system for many years and have always advised fans to leave adequate time to purchase tickets.
“Ahead of the weekend’s game with Fulham we are opening until 6pm on Thursday and Friday for fans to collect season tickets, who haven’t yet done so.
“We strongly advise those who have not yet collected not leave it until the hour before kick-off, as this could again cause unnecessary queues.”