The live departures board showed delays on key commuter services including the 7.42am service to Leeds to Chester, 7.46am service to York, 7.52am service from Leeds to Skipton and the 7.58am Leeds to Ilkley.
Some earlier services were cancelled due to a '"shortage of train conductors."
Other services started from different stations, such as Leeds instead of York, due to "more trains than usual needing repairs at the same time."
Commuters users shared their frustration with the new timetable on social media.
David Crawford said on Twitter: "First day of new train timetable - ‘more trains, faster services’. 7.00 to Leeds cancelled!! #northernfail"
Oliver Redfern said: "Translation: Northern cancel *all* services from Mytholmroyd to Manchester on Sunday’s, delete a Monday service into Leeds, and on top of that they can’t even get the first two Monday morning trains out on time - shame on you Northern Rail."
Twitter user Gregs50 said: "From what i can see of the 12 trains scheduled between Huddersfield and Leeds between midnight and 8 a.m. today 8 (EIGHT!!) cancelled, scandalous."
Mick Donelan said: "What a great start to new timetable all trains delayed 2 cancelled and 2 carriages on Leeds train - this'll be fun."
Chris Freeman said: "So new timetable and now i have no northern trains to Leeds #confused"
Katie Edmondson said: "New timetable ! First direct train from #Slaithwaite to #Leeds ... cancelled! Can I ask why?!"