Doheny was born in Northfield, Vermont, in 1873. He started his professional baseball career with the New York Giants of the National League (NL) in 1895. He signed with the team in September, and that year, he had a win–loss record of 0–3 and a 6.66 earned run average (ERA).
In 1896, Doheny went 6–7 with a 4.49 ERA. In 1897, he went 4–4 with a 2.12 ERA. In 1898, Doheny went 7–19 with a 3.68 ERA and led the NL with 19 wild pitches. In 1899, he went 14–17 with a 4.41 ERA and led the NL with 37 hit by pitches and 21 wild pitches. In 1900, he went 4–14 with a 5.45 ERA. In 1901, he went 2–5 with a 4.50 ERA before the Giants released him in July.
Later that month, Doheny signed with the NL's Pittsburgh Pirates. During the rest of the year, he went 6–2 with a 2.00 ERA and helped the Pirates win the NL championship. In 1902, he went 16–4 with a 2.53 ERA and helped the Pirates win the NL championship again.

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