We investigate the three-dimensional fractionally dissipated primitive equations with transport noise, focusing on subcritical and critical dissipation regimes characterized by $ (-Δ)^{s/2} $ with $ s \in (1,2)$ and $s = 1$, respectively. For $σ>3$, we establish the local existence of unique pathwise solutions in Sobolev space $H^σ$. This result applies to arbitrary initial data in the subcritical case ($s \in(1,2)$), and to small initial data in the critical case ($s=1$). The analysis is particularly challenging due to the loss of horizontal derivatives in the nonlinear terms and the lack of full dissipation. To address these challenges, we develop novel commutator estimates involving the hydrostatic Leray projection.