Emergency services were called to a section of the railway between Bradford Interchange and New Pudsey at around 9.30am.
Although no details have yet been released about the nature of the incident, it did result in services being temporarily halted.
Services affected include Northern trains between Preston and York as well as those between Leeds and Manchester Victoria or Huddersfield.
Lines reopened at around 10.30am but Network Rail warned that there would be disruption to services until around noon.
It said: "Emergency services have been able to deal with the incident between allowing lines to reopen.
"Whilst services recover, trains may be cancelled, delayed or revised.
West Yorkshire Police said the incident was being dealt with by British Transport Police.