The men, aged 52 and 21, have been arrested by Counter Terrorism Policing North East on suspicion of being concerned in the commission, preparation or instigation of acts of terrorism under section 41 of the Terrorism Act 2000.
The pair have been detained at a police station in West Yorkshire for questioning. Two residential addresses in Savile Town are being searched in connection with the ongoing investigation.
A statement by the Counter Terrorism Unit said: "We appreciate local people may have concerns as a result of this activity and we are grateful for their patience and understanding while these enquiries are carried out.
"We would also like to reassure them that the arrests were pre-planned and part of a proactive, intelligence-led investigation by Counter Terrorism Policing North East. Anyone with concerns is asked to contact their local neighbourhood policing team on 101.
"These arrests are not connected to the ongoing CT investigation into malicious communications."
West Yorkshire Police Superintendent for the Kirklees Area Marianne Huison said: "I understand our local communities will have concerns about this morning’s police activity but I want to offer my reassurance that we will continue to serve and protect the public of West Yorkshire. ã€€
"We work very closely with our colleagues in CT Policing North East and with local partners and we will ensure we maintain these strong links in order to provide a high level of service and delivery to everyone in our community. Public safety is our utmost concern”