A new class of poly(1,3,4-oxadiazole)s (PODs) with pendant phosphonic acid groups was synthesized via direct polycondensation of dicarboxylic acids and their dihydrazides using ionic liquid, namely 1-methyl-3-propylimidazoluium bromide ([mpim]Br), as a reaction medium, and triphenyl phosphite as a reaction activator. The polymers were obtained with inherent viscosities equal to 0.46–0.58 dL/g in two steps starting from polyhydrazides formation followed by thermal polycyclization under high vacuum. Polymers derived from 5-phosphonoisophtalic acid were soluble in traditional organic solvents, while application of 2-phosphonoterephthalic acid resulted in formation of insoluble gels. Such properties as thermal stability, glass transition temperatures, water uptake, molecular weights and proton conductivity of novel polymers were investigated in detail. A comparison between common poly(1,3,4-oxadiazole)s and their phosphorylated or phosphonated analogs having the same polymer backbone demonstrated that PODs with pendant phosphonic acid groups possess approximately the same thermal stability, but greater glass transition temperatures along with reduced solubility. Transparent flexible films cast from such novel polymers were characterized by high tensile properties, namely tensile strength of about 90–100 MPa and elongation up to 8%. The proton conductivity values measured at the temperature range from 20 to 90 °C varied from 4 × 10 −7 to 5 × 10 −6 S/cm at 100% relative humidity.