In a waterproof structure of an electrical junction box which renders the electrical junction box waterproof by bringing a stepped section 16 of a cover 2 into contact with a flange section 21 of a case 3, a protuberance 23 to be brought into pressing contact with the stepped section or the flange section is formed along the periphery of the stepped section 16 or the flange section 21. In order to provide effective sealing, the leading edge of the protuberance 23 is brought into line contact with the flange section 21 or the stepped section 16. Further, a skirt wall 13 is formed so as to extend downwardly from the stepped section 16, and a second skirt wall 22 is formed so as to extend from the flange section 21 along the skirt wall 13.