The disappointing 2-0 defeat means the Manchester United and England legend has now lost both games he has taken charge of since taking over as manager earlier this month.
Liam Delap and Jaden Philogene scored either side of the interval to hand Hull a comfortable victory at St Andrews.
Birmingham registered 14 shots on goal but only four on target as Hull picked up their fifth win of the season to move up to eighth.
The former Derby County and DC United boss saw his side beaten 1-0 at Middlesbrough on Saturday but the manner of Wednesday night's reverse got one fan raging at the 38-year-old.
According to ESPN, a fan made a beeline at the Blues boss as he was heading towards the tunnel at full time, shouting: "F*** off back to America."
Read more on Wayne Rooney
Key Arsenal coach who worked with Gareth Bale and Wayne Rooney seen as man to save Ajax
Rio Ferdinand wishes Wayne Rooney 'happy birthday' in the only way possible
Frustration appears to be boiling over quickly for Rooney who is yet to register a goal since taking over as manager.
His two results have been in stark contrast to the previous two games which saw Birmignham pick up a maximum six points against West Brom and Huddersfield under former boss John Eustace.
Eustace was dismissed after 15 months in charge and with Birmingham in sixth place in the Championship.
But the Midlands club now find themselves in 12th and facing a tough run of fixtures against promotion hopefuls, Southampton, Ipswich and Sunderland.
Most read in Championship
Tonali handed ten-month ban that rules Newcastle's £55m transfer out for the season
Why is Man United vs Man City kicking off an hour early? Huge derby moved to unique slot
'Classless' Simeone slammed for 'disrespectful' handshake with Rodgers after Celtic draw
Man City questioned for 'horrendous' pre-match outfit that not even Grealish could rock
Birmingham co-owner and NFL legend Tom Brady attended the defeat against Hull and watched on as fans booed after the full-time whistle, leaving any previous hopes of promotion in limbo.