16 of 52 services are currently at least 30 minutes late or cancelled according to trains.im information (correct at 7.40am).
Commuters took to social media to complain about the delays this morning.
Many are travelling home for Christmas or into the office for their final day at work.
Kieran Ingleton said: "This is crippling the north and it’s big Christmas get away today as well!"
Jude Harrison said: "So sick of delays and cancellations every single day.
Another user added: "I am sick to death of transpennine express constantly cancelling their trains."
Speaking on Wednesday, Managing director of TPE Leo Goodwin said: "I am really sorry for the disruption to our customers journeys. I know what a busy time it is whether people are trying to get to work, trying to get home to see school plays, visiting loved ones or trying to go out and enjoy their Christmas parties.
“Due to a number of issues with crew training caused by the late delivery of some of our new trains, along with a maintenance backlog and some infrastructure issues we have had to implement a temporary timetable, cancelling some journeys along one of our routes. This has unfortunately made a number of other services a lot busier. We are working really hard to sort this for our customers and as we introduce more new trains we should see an improvement to people’s journeys.”