Nutritional quality of a dietary fat is greatly influenced by fatty acid composition of a specific food. Caprine milk is known to have significantly high amounts of short chain and medium chain fatty acids (MCT). The objective of this study was to compare fatty acid compositions of non-fortified control (NC) with those of 2 types of iron fortified [regular ferrous sulfate (RFS) and large microencapsulated ferrous sulfate (LMFS) salts added] caprine Cheddar cheeses stored under different storage times and temperatures. Three batches of NC, RFS and LMFS cheeses were manufactured using the goat milk taken from the bulk tank of the Georgia Small Ruminant Research and Extension Center, Fort Valley State University, Fort Valley, GA. Iron was fortified for RFS and LMFS cheeses by addition of 8.23g and 9.03g Fe per 9 kg cheese, respectively at milling step, formulating 16% Fe in both forms of ferrous sulfate. Each batch of the cheeses were subdivided into 3 groups, packaged in 2”x3” plastic pouches, and stored for 0, 2 and 4 mo at 4 and −18°C. Results showed that palmitic acid (C16:0) content was the highest in all treated cheeses, followed by C18:1, C18:0, C14:0, C10:0, C8:0, C12:0 and C18:2 acids. The lauric:capric acid (C12:10) ratio was 0.40, which is unique to caprine milk and lower than that of bovine counterpart. Significant (P < 0.05 or P < 0.01) differences were found between cheese types and between storage periods in levels of all tested fatty acids except C16:1, C20:0 and C24:0 acids. Fatty acid contents of RFS and LMFS cheeses tended to be higher at longer storage time (4 mon) than those of initial NC samples. The 2-way interactions of cheese type x storage temperature, cheese type × storage period and storage period × temperature had significant (P < 0.05 or P < 0.001) effects on C10:0, C12:0; C6:0, C8:0, C18:2; and C4:0, C6:0, and C14:0 concentration, respectively. Storage temperature showed significant effect on C10, C12, C14, C14:1 and C18:1 levels. It was concluded that iron fortification and longer storage periods had significant effects on fatty acid levels than those of fresh control caprine milk Cheddar cheese samples.