The settlement spread in the area of the present Seinäjoki during the first half of the 16th century. During the 1550s there is said to have been three houses in Seinäjoki, Marttila, Jouppi and Uppa houses. House of Jouppila, which separated from the house of Jouppi, was established during the same century. All of the houses were located on the shore of the river.
Seinäjoki belonged to the church parish of Ilmajoki like Kurikka, Kauhajoki, Jalasjärvi and Alavus. However, in the 18th century the roads from Seinäjoki to the Church of Ilmajoki were usually in poor condition. Therefore, the inhabitants of Seinäjoki and neighboring Nurmo built together a new chapel in 1725 which in 1765 led to the formation of the chapel town of Nurmo. Seinäjoki, which after the Greater Wrath was called Alaseinäjoki, became a part of the chapel town. The chapel parish of Peräseinäjoki was founded in 1798, and the village of Alaseinäjoki was started to be called Seinäjoki again. The very same year, Östermyra steel mill was founded on the shore of Seinäjoki-river.
In the 1850s the actions to separate Seinäjoki from the church parish of Nurmo began. Ilmajoki wanted to connect Seinäjoki back to its own parish. In spite of the hard opposition of the inhabitants of Nurmo, the Senate of Finland accepted the petition from the inhabitants of Seinäjoki in 1863, to form an own chapel congregation. Seinäjoki got an independent local government in 1868. In 1900 Seinäjoki became an independent municipality.
Seinäjoki has grown around few important railroad crossings. Tampere – Vaasa railway which goes through Seinäjoki was inaugurated in 1883. The track, with the Kokkola track that has been opened for rail service in 1885, alongside the Kristiinankaupunki track which had been completed in 1913 raised Seinäjoki as an important railway crossing section in Finland. In the early 1970s the direct railway opened from Tampere to Seinäjoki and the services of
