Italian national Claudio Berardelli was cleared of charges of conspiring to harm Jeptoo's career by administering a banned substance. An assistant coach who worked with Berardelli and a pharmacist were also cleared of the charges in the Kenyan capital Nairobi.
They were arrested and released on bail more than a year ago.
Jeptoo, a three-time Boston Marathon and two-time Chicago Marathon winner, tested positive for EPO in an out-of-competition test in September 2014, just before she was due to claim a $500,000 prize as the top marathon runner in the world.
She was initially banned for two years but the sanction was increased to four years last year.
The Kenyan court ruled that prosecutors failed to prove that Berardelli and his co-accused were responsible for providing and administering the EPO while they were working with Jeptoo.
The three went on trial in Kenya despite a Court of Arbitration for Sport ruling last year that found Jeptoo received the EPO in an injection or injections from an unnamed doctor and hid her doping from her coaching team.