Salmonella enterica subsp. enterica serovar Enteritidis is one of the most common zoonotic pathogens. Specifically, Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) represented 61.2% of all reported serovars of confirmed human cases in 2017 in the European Union and about 70% of all reported serovars of confirmed human cases in 1988-2018 in Russia. Chickens known to be the main reservoir for S. Enteritidis (EFSA and ECDC 2018). However, there is a lack of information on full-genome sequences of S. Enteritidis, isolated in Russia. We report here the genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis S-25048 isolated from chicken (Gallus gallus domesticus) meat in Artyom, Russia. The assembled genome size was 4,695,145 bp. A total of 4,565 coding genes, 4 rRNAs, 62 tRNAs, and 14 noncoding RNAs were predicted. To our knowledge, this is the first publically deposited annotated genome of this serovar isolated from chicken in Russia. The Salmonella Enteritidis S-25048 genome is suitable for use as a reference strain of Salmonella Enteritidis isolated in Russia.