Gmina Czernikowo is a rural gmina (administrative district) in Toruń County, Kuyavian-Pomeranian Voivodeship, in north-central Poland. Its seat is the village of Czernikowo, which lies approximately 24 kilometres (15 mi) south-east of Toruń.
The gmina covers an area of 169.37 square kilometres (65.4 sq mi), and as of 2006 its total population is 8,378.
Gmina Czernikowo contains the villages and settlements of Czernikówko, Czernikowo, Jackowo, Kiełpiny, Kijaszkowo, Liciszewy, Makowiska, Mazowsze, Mazowsze-Parcele, Osówka, Pokrzywno, Skwirynowo, Steklin, Steklinek, Witowąż, Wygoda and Zimny Zdrój.
Gmina Czernikowo is bordered by the towns of Ciechocinek and Nieszawa, and by the gminas of Bobrowniki, Ciechocin, Kikół, Lipno, Obrowo, Raciążek and Zbójno.