Rising from number 111 last year, Apple's profits grew by almost $12 billion (£7.7 billion) in a year that saw the death of co-founder Steve Jobs and Tim Cook taking the reins as CEO.
The top tech firm on Fortune's list, however, was Apple rival and patent foe Samsung, which landed at number 20, up from 22 last year.
In addition to besting Nokia as the world's top phone manufacturer, Samsung also sold nearly 48 million TVs for 27 per cent of that market, Fortune said.
Also topping Apple were HP (31), AT&T (32), Hitachi (38), and Verizon (50). Apple's main supplier, Taiwanese company Hon Hai, was ranked 43rd, boasting total revenues of $117.5 billion (£75.7 billion).
According to Fortune, the Cupertino-based company saw an 85 per cent change in profits from two years ago, claiming almost $23 billion (£14.8 billion) in fiscal 2011 earnings, and more than $108 billion (£69.6 billion) in total revenues.
The list's top five companies are Shell, Exxon Mobile, Wal-Mart, BP, and China's Sinopec Group.
Apple earned the title of most reputable company of the year in February, according to a Harris Interactive report. Based on its "hybrid status as a technology/consumer product/retail company," it scored an 85.62 on the list, topping Google, which was ranked at number one last year.