Modern Merzifon is a typical large but quiet Anatolian town with schools, hospitals, courts and other important infrastructure but few cultural amenities.

Scholar Özhan Öztürk, however, claims that original name was Marsıvan (Persian marz 'border + Armenian van 'town') which means "border town".

Archaeological evidence (hundreds of burial mounds or höyüks) indicates settlement of this well-watered area since the Stone Age (at least 5500 BC).

From 600 BC the Phrygians were pushed out by further invasions from the east, this time by Cimmerians from across the Caucasus mountains; graves from this period have been excavated and their contents displayed in the museum in Amasya.

The district of Amasya was destroyed during civil wars of the Roman era but Merzifon was restored by command of the emperor Hadrian.

In 1915, over 11,000 Armenians were deported from the city (which had had approximately 30,000 inhabitants in the previous year) in death marches; others were killed and their property confiscated and sold to Turkish insiders, supposedly to benefit the Ottoman war effort, as documented by missionary George E. White.

British troops were deployed in formerly Ottoman lands to ensure the terms of surrender, and some of them arrived in Merzifon in 1919 just as George White returned and reopened the college and orphanage, as well as a new "baby house" for displaced Armenian mothers and infants.

Merzifon's main attraction is the Merzifonlu Kara Mustafa Paşa Mosque, built in 1666 and featuring one of the lovely şadırvans (ablutions fountains) with internally painted domes for which the Amasya area is known.