Services were cancelled or delayed for much of the day after criminals struck between Wakefield Westgate and Swinton, in Rotherham.
Northern said the incident caused some lines to be blocked, affecting services between Leeds and Sheffield and Doncaster.
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The operator said all lines were fully reopened and services were able to return to normal early this afternoon.
British Transport Police said no one had yet been arrested in connection with the incident but investigations were ongoing and patrols in the area had been stepped up.
Anyone with information is asked to text BTP on 61016 or call 0800 40 50 40.