His playing career started in 1982 at Vardar Skopje where he quickly developed into one of the most feared strikers in the Yugoslav League, becoming league top scorer in the 1983–84 season. The skill and seeming ease of his goal scoring exploits in Skopje made him a target for bigger clubs.

During summer 1988, Pančev was snapped up by Red Star Belgrade, which beat cross-town rivals FK Partizan to the twenty-two-year-old’s signature. Another talented youngster, 21-year-old Dejan Savićević, also arrived to the club during the same transfer window, but both promptly got sent to serve the mandatory Yugoslav People’s Army (JNA) stint that kept them off the pitch for the entire league season.

Pančev debuted for his new club in 1989 and played three full seasons for crveno-beli, scoring an incredible 84 goals from 91 league appearances, and winning the European Cup and the Intercontinental Cup in 1991.

Pančev played in the 1990 World Cup for Yugoslavia and scored two goals in their 4–1 win over the United Arab Emirates in the group stage. It proved to be the only international tournament he played in; he was later called to UEFA Euro 1992, but he then renounced a place in the squad on May 23, claiming physical reasons, although this statement was believed for just a few people in Belgrade, who saw political views as the true cause of the withdrawal of the Macedonian forward – who had been the top marksman on qualifying group stages, with ten goals. He was replaced on the same day by Dragan Jakovljević, but in May 31 the national team was banned due to Yugoslav wars, just ten days before the tournament opening.

Due to his phenomenal strike rate, during the early 1990s, he was widely recognized as one of the best strikers in the world. Displaying great goalscoring instincts and predatory skills, he got nicknamed Kobra by the Serbian sports media. Red Star fans remember him as the player who scored the winning penalty in the 1991 European Cup Final, bringing Red Star the most prestigious trophy in European football for the first time in its 50-year existence.

On 4 March 1992, Pančev scored two goals for Red Star to defeat Panathinaikos 2–0 at the Olympic Stadium in Athens in a European Cup match. The spotlight was on him because upon completing the forms to gain entry in Greece, he wrote his nationality as Macedonian. This made great havoc among the Greeks, he was detained several hours before being allowed to cross the border. In an interview after the duel he would say, “There is a saying that luck follows the brave. I was happy to score two goals before 80,000 spectators in Athens and Red Star to win 2–0. After that, the earth could open up and I did not mind.”

However, in contrast to club president Pellegrini, head coach Bagnoli wasn’t as taken with Pančev’s playing style and already during pre-season reproached the player for lack of movement. Once the season started, Pančev’s performances were nowhere near expectations. From the get go, it was apparent the Macedonian was experiencing major problems adapting to stringent Italian league defences and his goal output suddenly became nonexistent. It didn’t take long for his relationship with Bagnoli to take a turn for the worse, as the two started butting heads, often publicly. Pančev apparently even resorted to faking an illness in order to avoid sitting on the bench. The Italian press got down on the striker too, derisively modifying his Red Star moniker Il Cobra to Il Ramarro (green lizard). He’d wait until after the winter break to net his first league goal, which came at home versus Udinese in January 1993. Parallel to Pančev’s struggles, Inter posted a decent league season behind Sosa’s goalscoring exploits, and with no distraction of European football finished league runners-up to cross-town rival AC Milan. Overall, during his debut season, Pančev appeared in just twelve league matches for the nerazzurri, scoring one league goal in addition to five goals in four Coppa Italia appearances (second best striker of the latter competition).

Pančev later played in the Macedonian national team’s first ever official match, on 13 October 1993, against Slovenia. His final international was a June 1995 European Championship qualification match against Belgium.

Pančev remained part of the Inter squad for the 1993–94 season, although he was completely out of the first-team picture as his relationship with Bagnoli deteriorated to a point of no repair. Furthermore, the arrival of £12 million signing Dennis Bergkamp from Ajax relegated the Macedonian even further down the pecking order. He did not get any league appearances during the first half of the season nor did he get any action in the UEFA Cup. In January 1994, during the winter break, he got loaned out to German team VfB Leipzig.

Pančev returned to San Siro following a six-month loan hoping to make the most of his second chance. Playing under new head coach Ottavio Bianchi, the 29-year-old looked on track to do just that early into the season, scoring in a 3–1 home win versus Fiorentina and two weeks later in a 1–2 home loss to Bari. However, subsequent loss of form and injuries meant that he made the total of only seven league appearances during the campaign. He also scored twice in Coppa Italia. In the UEFA Cup, he got a surprise starting appearance in late September in the return leg of the second round tie versus Aston Villa and even had a glorious opportunity to score following Nicola Berti’s thundering shot that bounced favourably off the crossbar, but ended up blasting the rebound high over the bar. UEFA Cup title-holders Inter ended up getting eliminated on penalties that night. It was Pančev’s first and only European match while at Inter. Throughout the season, the entire club was going through major turmoil behind the scenes and eventually, the owner and club president Pellegrini sold the team to oil magnate Massimo Moratti in March 1995. At the end of the season, during the summer 1995 transfer window, Pančev got offloaded to Fortuna Düsseldorf.

He ended his playing career to Swiss team Sion in 1997.

After retiring from playing, Pančev often talked at length about his failed stint at Inter. In 2002, he addressed the criticism he often received in Italy about his lack of movement off the ball:

In November 2003, to celebrate UEFA’s jubilee, he was selected as the Golden Player of Macedonia by the Football Federation of the Republic of Macedonia as their most outstanding player of the past 50 years.

Pančev was the highest scorer in top-division European football in the 1990–91 season with 34 goals, and should have won the European Golden Boot award. However, UEFA decided to make the competition unofficial for the season because of suspect scoring sprees in Cyprus. Pančev did not get the prize at the time, but received it fifteen years later on 3 August 2006 in Skopje. The Golden Boot was presented at a special gala by Michel Platini, Dragan Stojković and Dragan Džajić.

After retiring from playing, Pančev worked with the Football Federation of Macedonia. In July 2006, Pančev was named the sporting director of Vardar.