This paper presents a study to identify and assess the challenges of cotton production in the Tolon District of the Northern Region. This is an applied research study of a descriptive-surveying kind .The objectives of this research is to; assess the level of Capacity building that cotton farmers have received to boost production during the past decade (2002 – 2012), assess the quality of inputs given to cotton companies, to identify and assess farmers concerns over the system of recovery of inputs cost to farmers in the Tolon District within the period, and to determine whether prices paid for seed cotton over the years afford farmers a surplus income. Cotton production in Ghana started in 1968 under the control of the Cotton Development Board of the Ministry of Agriculture and performed its function effectively until 1977 when production began to fall due to declining producer prices relative to food crops. Indications are that Ghana achieved high level of production before other neighboring countries in West Africa who started production before her. About 75.0% of the farmers are from the ages of 36 years and above. About 55.0% of the cotton farmers in the district do not have any formal education. The mean dependency ratio of the farmers stands at 8.1. It was found that more than 80% of the famers cultivate only 1-2 units of land. All the respondents receive inputs from the company but none is by the Government. The analysis showed that none of the farmers received any extension service form the Ministry of Agriculture or from any government source. The incomes of the farmers are quite low, mostly below GH₵1000.00 per annum. They generally depend on the household for labour on their farms. Delay delivery, poor quality pesticides and erratic rain fall are the major challenges facing cotton production in the Tolon District of the Northern Region of Ghana.