[2] Epiphaneia's dam Cesario was an outstanding racemare who won the Yushun Himba and the American Oaks and was voted the JRA Award for Best Three-Year-Old Filly in 2005.

[4] Epiphaneia made his three-year-old debut in the Grade II Hochi Hai Yayoi Sho over 2000 metres at Nakayama Racecourse in which he was ridden for the first and only time by William Buick.

Starting at odds of 5.1/1 in an eighteen runner-field he finished second again, beaten half a length by Kizuna, with Apollo Sonic, Peptide Amazon, and Logotype in third, fourth and fifth.

[5] After the summer break, Epiphaneia returned in the Grade II Kobe Shimbun Hai (a trial race for the Kikuka Sho) over 2400 metres at Hanshin on 22 September.

He tracked the pace-setters Bande and Neko Taisho before taking the lead 400 metres from the finish and recorded his first Grade I success, beating Santono Noblesse by five lengths.

Later that month, the colt represented Japan in the Queen Elizabeth II Cup at Sha Tin Racecourse in Hong Kong.

[9] On his first appearance of his autumn campaign, Epiphaneia contested the Tenno Sho over 2000 metres at Tokyo and finished sixth of the eighteen runners behind the five-year-old Spielberg.

Christophe Soumillon took over the ride from Fukunaga when Epihaneia contested the 33rd running of the Japan Cup over 2400 metres in front of a crowd of 100,186 at Tokyo on 30 November.

The locally trained runners included Gentildonna, who was attempting to win the race for an unprecedented third time, Just A Way, Harp Star, and Spielberg.

[10] The Arima Kinen over 2500 metres at Nakayama Racecourse on 28 December attracted its customary strong field, and Epiphaneia started second in the betting behind Gold Ship, with the other contenders including Just A Way and Gentildonna.