Dinucleoside polyphosphates, Np(n)N', exert their physiological effects via P2 receptors (P2Rs). Np(n)N' are attractive drug candidates as they offer better stability and specificity compared to nucleotides, the most common P2R ligands. To further improve the agonist properties of Np(n)N', we synthesized novel isosters of dinucleoside polyphosphates where N and N' are A or U and where the Pα or Pβ phosphate groups are replaced by boranophosphate, denoted as Np(n)(α-B)N' or Np(n)(β-B)N' (n = 3, 4), respectively. The potency of Np(n)(α/β-B)N' analogues was evaluated at tP2Y(1), hP2Y(2), hP2Y(4), and rP2Y(6) receptors. The most potent P2Y(1)R and P2Y(6)R agonists were the Up(4)(β-B)A (A isomer, EC(50) of 0.5 μM vs 0.004 μM for 2-SMe-ADP) and Up(3)(α-B)U (B isomer, EC(50) of 0.3 μM vs 0.2 μM for UDP), respectively. The receptor subtype selectivity is controlled by the position of the borano moiety on the Np(n)N' polyphosphate chain and the type of the nucleobase. In addition, Np(n)(α/β-B)N' proved ∼22-fold more resistant to hydrolysis by e-NPP1, as compared to the corresponding Np(n)N' analogues. In summary, Up(4)(β-B)A and Up(3)(α-B)U are potent, stable, and highly selective P2Y(1) and P2Y(6) receptor agonists, respectively.