For qualification for the second edition of the Asian Championship, Iran was drawn into a group with Israel, India and Pakistan. Qualification began in the summer of 1959 in Kochi, India where due to the high humidity, matches were played for 80 minutes each. Iran had an ideal start to qualification, defeating the defending champion Israel 3-0 courtesy of goals by Hajari, Barmaki and Dehdari. This win was followed by two defeats against Pakistan and India, 4-1 and 3-1 respectively with goals coming from Haji-Mokhtar ad Dehdari. The return matches, also in Kochi, began with a 1-1 tie with Israel and Hajari scoring. Iran avenged both first leg losses by defeating Pakistan 4-1 (hat trick by Hajari and one by Jamali) and India 2-1 (brace by Dehdari). In spite of these victories, Iran finished in second place, trailing Israel by a single point and failed to qualify for the Asian Championship.

Once again financial issues proved problematic and transportation funds from the IFF never materialized resulting in the national team watching the 1962 Asian Games at home.

Qualification for the 1964 Olympics in Japan started with Iran facing Pakistan, Iraq and India as other Olympic hopefuls and the games being played on a home and away basis. In the 1st game at home against the Pakistani squad, Iran opted for an offensive 4-2-4 formation and in spite of numerous attacks in the first 15 minutes, surprisingly it was Pakistan who opened the scoring on a counterattack. But such a lead did not last long for Pakistan as Iran stormed back with four unanswered goals by Shahrokhi, Shirzadegan and Behzadi (2) to win the match 4-1. Behzadi's second goal (and Iran's fourth) was especially astonishing as he turned his body in mid air and hammered home a cross with a thunderous downward header. In the return leg a month later, although a 1-0 victory for Pakistan on a goal that seemed to come off of an uncalled foul spelled defeat, however, the margin of victory in the first leg proved sufficient to send Iran to the next round.

Next up was Iraq who took the Amjadieh field in the Fall. Iran's only change in its lineup was replacing Shahrokhi with Amir Asef while such regulars such as Asli, Dehdari, Ranjbar, Shirzadegan and Behzadi once again represented Iran on the field. A goal by Arab and a hattrick by Shirzadegan and an ultimate 4-0 win rendered the return match meaningless. A 0-0 tie in Baghdad confirmed Iran's overall supremacy thus leaving only India in Iran's path to the Olympics. In a jam-packed Amjadieh Stadium 35,000 fans had some concerns about injuries to Jamali, Saedi, Dehdari and Jasemian (who were in turn replaced by Latifi, Talebi, Barmaki and Habibi) but instead were treated to a 3-0 win over India with goals by Barmaki, Shirzadegan and Behzadi. Any hopes of a revival by India in the return match were squashed when Iran cruised to another victory this time by a 3-1 score with goals by Behzadi (2) and Shirzadegan and thus earned its ticket to the Olympics.

For the 1964 Asian Championship qualifiers, Iran was grouped with Sri Lanka, India and Afghanistan. The games were to be played either home and away or on a neutral site but due to political reasons (some sources state problems with India while others mention the finals being held in Israel) all teams but India withdrew.

With the sweet qualification campaign for the Olympics still fresh in everyone's memory, internal problems started to brew. A trip to the Soviet Union for some friendlies had the IFF and club team Shahin clashing over coaching decisions and as a result six Shahin players were banned from playing for the national team (although some claim the exclusions were for political reasons). Already depleted by the absence of Barmaki, Behzadi, Shahrokhi, Shirzadegan, Jasemian and Vatankhah for its Olympic matches in Japan, Ranjbar also withdrew from the squad due to personal reasons. Fekri, the team coach at the time had no choice but to bring in younger players such as Mostafavi, Ghelichkhani and Esmaeili as replacements and while these seven new players had potential but they had yet to experience the high paced game of international soccer, specifically that of East Germany, Mexico and Romania.

The result was catastrophic. A German side who seemed superior in all aspects did as it pleased en route to a 4-0 victory. Iran regained some pride in its 2nd game in a well fought 1-1 tie with Mexico with our equalizing goal coming from the penalty spot by Nayyerloo. One of the more talked about scenes from the game was the discovery of a hole on the field and the 10 minutes it took to fill it up. A win against Romania in the final group match would have left a mathematical chance of advancing depending on the result of the East Germany-Mexico match, but in spite of a solid performance, it was the Romanians who prevailed by a score of 1-0. Thus Iran ended its games by finishing last in the group and was eliminated in the first stage of its 1st Olympic venture.

Iran roster: Asli, Bayati, Mirzaei, Arab, Habibi, Mostafavi, Latifi, Jamali, Talebi, Noorian, Nayyerloo, Fanaei, Esmaili, Ghelichkhani, Amirasefi, Saedi, Khodaparast. Coach: Fekri

In the 1966 Asian Games, Iran was grouped with Burma, Japan and Malaysia and in a tense and physical match, opened its campaign against Malaysia. Goals by Shirzadegan and Behzadi gave Iran full points. Iran next faced Japan. Late in the first half, Shirzadegan gave Iran the lead with a well timed shot and went to the break with the lead. The second half started with both teams intensifying their physical play resulting in numerous fouls and ultimately an equalizing and subsequent leading goal by the Japanese. Moments later Aziz Asli, Iran's keeper, collided with a Japanese player which resulted in a penalty kick. The call was protested by Mohammad Ranjbar, Iran's captain, which lead to his sending off. Japan converted and went on to win the game 3-1. Upon its conclusion, Hossein Mobasher, IFF's representative, entered the field to voice his dissatisfaction with the ref's decisions, however, it resulted in a bench-clearing brawl by both teams which even had the spectators involved. When the dust finally settled, IFF announced that they were withdrawing from the tournament and returning to Iran, however, due to traveling issues, the return trip did not take place and Iran faced India in its final group game. Needing a win to advance, behind goals from Fariborz Esmaeili (twice), Ali Jabbari and Jalal Talebi, India was defeated 4-1, sending Iran to the quarterfinal group phase.

Grouped with Burma and Indonesia and with the top two teams advancing to the semifinals, Iran took the field against Indonesia. In the first half, following a foul on Esmaeili, Iran earned a freekick which Behzadi perfectly curled beyond the Indonesian wall and into the net. A tense, defensive effort preserved the lead and 1-0 result. In the next match Iran fell victim to Burma's speed and conceded the game's only goal in a 1-0 loss but by virtue of its previous win advanced into the semifinals to face the top team of the other group, Japan. This game was unlike the 1st game between the two teams and was played at a high level with both teams attacking each other's goal, but it was Esmaeili's shot that finally broke the deadlock and in spite of Japan's increasing pressure, Iran managed to avenge the earlier defeat and advance to the championship game. The final was played against Burma with Iran attempting to utilize its height and aerial game and Burma its speed. While the game itself was fairly even, one single mistake determined the outcome. On a ball that probably should have been cleared by the defense, Asli left his goalline leaving Burma to score from one of the easiest opportunities. The game ended with a 1-0 win for Burma, giving them the championship and having Iran settle for silver medals.

Iran roster: Asli, Zelli, Jasemian, Hasan Habibi, Goodarz Habibi, Arab, Ranjbar, Shahrokhi, Aminkhah, Jabbari, Esmaeili, Talebi, Farzami, Ghelichkhani, Saedi, Mirza-Hasan, Behzadi, Eftekhari, Shirzadgan. Coach: Fekri

Many changes were ongoing within the country which directly impacted the national team. In the name of reorganizing sports as a whole the athletic division was being huddled from one department to another. In an effort to bring some stability to such departments it was proposed that previous Olympians lend their expertise in running the new structure smoothly. As a result rather than participate in the 1968 Olympics, athletes in all sports spent their time running offices and shuffling paperwork.