Modified from an earlier answer of mine

The US and Japan were both sovereign powers that recognized each other as such. This meant that Japan had various ambassadors and other diplomatic officials sent to the US, and vice-versa. In addition to these official appointments, there were also special envoys and other officials from each country. This was the norm for diplomatic relations between sovereign states in the modern era. Even when US domestic opinion favored avoiding foreign entanglements, Washington maintained an array of official contacts with the rest of the world. And this is what is usually meant by "isolationist." The US's position was not a total embargo from contact with the outside world akin to Japan under the Tokugawa Shogunate (and here too things were more complex than the country simply being closed off- see this thread by /u/NientedeNada on the problems of sakoku). The US government had an array of official contacts with sovereign governments, including Japan and Germany.

As for what was going on throughout 1940 and 41 between the US and Japan, there were diplomatic talks between the two countries to evade war between them. The Japanese initiated a good deal of this process. The Japanese Foreign Ministry had dispatched the IJN admiral Nomura Kichisaburō in November 1940 with the specific task of trying to smooth over US-Japanese relations. Kurusu Saburō joined Ambassador Nomura Kichisaburō as a special envoy in November 1941 to try and help to deescalate the growing tensions over Japan's continued war in China, its Tripartite Pact with Germany and Italy, as well as Japanese moves towards French Indochina. Both men were relative doves within the Japanese government and were aligned with the more cautious approach to foreign relations exemplified by Japanese PM Konoe Fumimaro. Both envoys dealt with US Secretary of State Cordell Hull and Japan's stated purpose of this diplomatic mission was to avoid war and preserve peace in the Pacific.

FDR's "Day of Infamy" speech maintained that the US was "at the solicitation of Japan, was still in conversation with its Government and its Emperor looking toward the maintenance of peace in the Pacific." FDR's speech was certainly presenting a very one-sided view of the Kurusu-Nomura negotiations in his speech. Japan was not the sole initiator of these talks and Hull certainly did his part in making sure that they broke down. The general US demands were for a suspension of Japan's war in China, Japan's breaking or loosening of the Tripartite Pact, and guarantees of Japan not to seize territory in the Pacific. These were not necessarily unreasonable goals on the part of the US but they were also ones that the highly divided Japanese government could never meet. Konoye's successor, Army Minister Tōjō Hideki, was not a man who could ever meet these demands as he was expansionist and a firm believer in the China war.

The net result of this impasse was that the Kurusu-Nomura mission could not meet Hull's demands and their counter-offers were neither accepted in Tokyo or Washington. Eventually the Japanese embassy delivered a note on 7 December indicating and that further negotiations were impossible. This was not a declaration of war per se, but one that signaled to all parties Japan's intent for war. Tokyo had intended for Nomura to deliver the note shortly before the Pearl attack, but such an important enciphered document had to be decrypted by non-expert staff, so the Japanese diplomats delivered the note to Hull during the Pearl Harbor attack. Unbeknownst the the Japanese, American Magic intercepts had actually decoded the Japanese messages before their intended recipients. So Hull knew exactly what the Japanese were going to deliver before they arrived in his office.

The Magic intercepts as well as the timing of the note led to a greater sense within Washington that Japan had simply used the Kurusu-Nomura mission as an attempt by Japan to play for time while it prepared for war. Not surprisingly, FDR would emphasize Japanese perfidy during his speech. There is some merit to these charges but they project a coherency and strategic foresight onto the Japanese decision-making that just was not present within the Japanese government. More often than not, the left hand did not know what the right was doing in the Japanese government, so ambassadors like Nomura were stuck having to engage in a diplomatic game where they had no real pieces and could not make any serious headway to preserve the peace.