Background/Objectives: Although physical activity and balanced diet may increase peripheral brain-derived neurotrophic factor (BDNF) concentration, little is known about whether these factors modify BDNF content in physically active individuals and whether the serum fatty acid (FA) profile is related. This study aimed to evaluate quality of diet, identify specific dietary patterns and assess their influence on BDNF and FA levels in serum. It is hypothesized that there is a correlation between diet quality and the concentrations of BDNF and FA in the serum of physically active male individuals. Methods: Physically active young adult male students at Jozef Pilsudski University of Physical Education in Warsaw (Poland) were enrolled. Dietary patterns were identified with cluster analysis and linear discriminant analysis (LDA) based on responses to a validated food frequency questionnaire, KomPAN® version 1.1. Results: Consumption of beverages, vegetables, milk, wholemeal bread/rolls, fruit and vegetable juices, butter, tinned vegetables and fruits were significant in the LDA model, in which three clusters were distinguished. Cluster 1 was characterized by more frequent consumption of wholemeal bread/rolls, milk, fruits, vegetables, fruit and vegetable juices and sweetened hot beverages and by significantly greater values for the pro-healthy diet index (p < 0.0001) and diet quality index (p < 0.0001) compared to Clusters 2 and 3. The diet of Cluster 2 was of the worst quality, as indicated by the higher values of the not-healthy diet index. Cluster 1 had the tendency for the highest BDNF levels (of the best quality of diet), and a tendency for decreased BDNF concentration with an increased physical activity level was observed. Conclusions: Physical activity, diet quality and BDNF level depend, correlate and interact with each other to provide both optimal physical and mental health.