The footpaths and the trails for running or traveling are increasing. But their English information is still under developing.
Footpaths
Googlemap _Footpaths in Hokkaido
The recommended paths as of their impressiveness,uniqueness,information accessibility are;
Nemuro Footpath(E,Co,J)
The east end of Hokkaido has a kind of the “world’s end” scenery. A group of diary farmers have maintained them. Their websites are useful.
Kitanemuro Ranchway(E,J)
“Kiraway”, the long trail 6 Stages over 70km, you can start your first step from Nakashibetsu Airport! Must see the website in spite of in Japanese. You can download their excellent maps too.
A ultra long trail over 200km “AKWay” is between Abashiri and Kushiro. But it mostly on roadway, and less information on the Internet.
Rebun Island Footpath(J)
Maybe trekking rather than footpath. Trip all around the northernmost isolated island, it must be memorable.
Toya Footpath(E,Cs,J)
The active volcanoes are just behind the spa town at lakeside. The paths are in the volcanoes’area never seen elsewhere. The maps for download are too cool.
Wakkanai Footpath(J): Soya Hills
The north end of Japan, Russia in your view from the windy hills.
25 Minutes from Sapporo by train. Good experience to feel real Hokkaido.
Also these are alternatives,