  The recent measurements of the direct CP asymmetries ($A_{CP}$) in the
penguin-dominated $B\to K \pi$ decays show some discrepancy from the standard
model (SM) prediction. While $A_{CP}$ of $B^+ \to \pi^0 K^+$ and that of $B^0
\to \pi^- K^+$ in the naive estimate of the SM are expected to have very
similar values, their experimental data are of the opposite sign and different
magnitudes. We study the effects of the custodial bulk Randall-Sundrum model on
this $A_{CP}$. In this model, the misalignment of the five-dimensional (5D)
Yukawa interactions to the 5D bulk gauge interactions in flavor space leads to
tree-level flavor-changing neutral current by the Kaluza-Klein gauge bosons. In
a large portion of the parameter space of this model, the observed nonzero
$A_{CP}(B^+ \to \pi^0 K^+) - A_{CP}(B^0 \to \pi^- K^+)$ can be explained only
with low Kaluza-Klein mass scale $M_{KK}$ around 1 TeV. Rather extreme
parameters is required to explain it with $M_{KK}\simeq 3\tev$. The new
contributions to well-measured branching ratios of $B \to K \pi$ decays are
also shown to be suppressed.
