In 1881 Japp became assistant professor at the Royal School of Mines and Normal School of Science South Kensington and in 1890 Professor of Chemistry at the University of Aberdeen.
In 1885 he was elected a Fellow of the Royal Society.He retired in 1918.
After the death of his only son in 1920 and an operation the following year, his health deteriorated.
He lost his eyesight in his final years, and died in 1925.
Japp had married Elizabeth Tegetmeyer of Nordhausen, Germany, with whom he had one son and two daughters.