He was generally considered a capable ruler, but ruled for less than two years before dying from injuries suffered from falling off a horse.
He received a number of official posts during Emperor Wenxuan's reign, and was said to have distinguished himself in his ability to govern despite his youth, and was known for his solemnity.
Emperor Wenxuan also favored irreverent and sometimes immoral games within his palace, but when Gao Yan was present he would curb his behavior, and while Emperor Wenxuan was known for often visiting nobles' households and having sexual relations with their women, regardless of their relationships to him, he did not do so as to Gao Yan's household.
Emperor Wenxuan's crown prince was his son Gao Yin, who was known for his studiousness, but Emperor Wenxuan, who, despite his Han ethnicity, favored Xianbei warrior ways, felt that Gao Yin was too Han in his thinking and repeatedly considered deposing him.
Particularly when he was drunk, Emperor Wenxuan often stated that he would pass the throne to Gao Yan, and he stopped doing so only after being warned by his prime minister Yang Yin that his statements were potentially causing instability.
He stated to his wife Empress Li Zu'e, "A person will live and die, and there is nothing to regret, other than that our son Gao Yin is still young, and someone else will take his throne."
Pursuant to Emperor Wenxuan's will, the government was in the hands of several of his trusted officials – Yang Yin, Gao Guiyan (高歸彥) the Prince of Pingqin, Yan Zixian (燕子獻), and Zheng Yi (鄭頤).
As Emperor Fei took the throne while he was attending to his father's deathbed at the secondary capital Jinyang (晉陽, in modern Taiyuan, Shanxi), when he proceeded to the capital Yecheng (鄴城, in modern Handan, Hebei) in spring 560, it was initially believed that Gao Yan or Gao Zhan would be put in charge of Jinyang—then perhaps the most militarily secure city in the empire; instead, by the arrangements of Yang and his associates, the two princes were ordered to accompany the young emperor to Yecheng.
Once the imperial train arrived at Yecheng, the situation became even more tense, as an associate of Yang's, Kezhuhun Tianhe (可朱渾天和), was convinced that Emperor Fei would not be safe in his reign unless his two uncles were killed, and alternatively, Yan Zixian considered putting Grand Empress Dowager Lou, who still wielded much power as the clan matriarch, under house arrest, and forcing her to turn her authorities to Empress Dowager Li.
Meanwhile, the ambitious Yang was carrying out a governmental reorganization scheme to trim unnecessary offices and titles and to remove incompetent officials.
Yang, Kezhuhun, Yan, Zheng, and Song Qindao (宋欽道) were all captured and severely battered.
Gao Yan's advisors, headed by Wang Xi and Zhao Yanshen (趙彥深), then suggested that he take the throne himself—noting to him that his actions in killing Yang and his associates meant that when Emperor Fei was grown, he would never be able to have a cordial relationship with Emperor Fei.
He entrusted much of his decision-making to Wang Xi, Yang Xiuzhi (陽休之), and Cui Jie (崔劼), often having them stay in the palace all day to examine the laws and regulations.
In spring 561, Emperor Xiaozhao had the former Liang dynasty general Wang Lin (who had fled to Northern Qi in 560 after his failed attempt, supported by Northern Qi, to let Xiao Zhuang rule as Liang's emperor, against Chen dynasty and the Northern Zhou-supported Western Liang), take up position at Hefei (合肥, in modern Hefei, Anhui), to plan a campaign against Chen.