The objective of the research study performed was to determine the effect of deep-freeze storage time and thawing method on the composition and profile of fatty acids in intramuscular fat of rabbit meat. The research material comprised 50 thigh muscles of the Californian rabbits slaughtered at the age of 110 days. The vacuum packed samples were stored under deep-freeze (-28 ± 1 °C) conditions for 2 weeks and for 3 months, and, next, they were thawed in a microwave oven or in air. In the muscles investigated, the profile of fatty acids was determined using a gas chromatography method. It was found that the prolongation of deep-freezing storage time (up to 3 months) caused the percent content of palmitic and stearic acids to increase in the intramuscular fat of thigh muscles thawed in air and the content of those compounds to decrease in the fat of muscles thawed in the microwave oven. The meat samples after 3-month deep frozen storage and thawed in air were characterized by the lowest percent content of oleic, linoleic, and α-linolenic acids. At the same time, it was found that the content of saturated fatty acids in that group increased and the content of mono- and polyenic acids decreased. This contributed to the negative modification in the fatty acid profile expressed by health quality indices. The most advantageous ratio of n-6/n-3 PUFA acids in the rabbit meat analyzed was found in the meat after 2 week deepfrozen storage and thawed in air.