The objective of this study was to estimate the genetic variation of ovine milk fatty acid (FA) composition. We collected 4,100 milk samples in 14 herds from 976 Churra ewes sired mostly by 15 AI rams and analyzed them by gas–liquid chromatography for milk fatty acid composition. The studied traits were 12 individual FA contents (proportion in relation to the total amount of FA), 3 groups of fatty acids [saturated fatty acids (SFA), monounsaturated FA (MUFA), and polyunsaturated FA (PUFA)], and 2 FA ratios (n-6:n-3 and C18:2 cis-9,trans-11:C18:1 trans-11). In addition, percentages of fat and protein and daily milk yield were studied. For the analysis, repeatability animal models were implemented using Bayesian methods. In an initial step, univariate methods were conducted to test the hypothesis of the traits showing additive genetic determination. Deviance information criterion and Bayes factor were employed as model choice criteria. All the studied SFA showed additive genetic variance, but the estimated heritabilities were low. Among unsaturated FA (UFA), only C18:1 trans-11 and C18:2 cis-9,cis-12 showed additive genetic variation, their estimated heritabilities being [marginal posterior mean (marginal posterior SD)] 0.02(0.01) and 0.11(0.04), respectively. For the FA groups, only PUFA showed significant additive genetic variation. None of the studied ratios of FA showed additive genetic variation. In second multitrait analyses, genetic correlations between individual FA and production traits, and between groups of FA and ratios of FA and production traits, were investigated. Positive genetic correlations were estimated among medium-chain SFA, ranging from 0 to 0.85, but this parameter was close to zero between long-chain SFA (C16:0 and C18:0). Between long- and medium-chain SFA, estimated genetic correlations were negative, around −0.6. Among those UFA showing significant additive genetic variance, genetic correlations were close to zero. The estimated genetic correlations among all the investigated FA, milk yield, and fat and protein percentages were not different from zero. Our results suggest that low additive genetic variation is involved in the determination of the FA composition of milk fat in Churra sheep under current production conditions, which results in low values of heritabilities.