Founded in 1986, the team played its final year in the second tier of the United States soccer pyramid in the NASL Conference of the USSF Division 2 Professional League coached by Teitur Thordarson.

On March 19, 2009, an ownership group led by principal Greg Kerfoot was granted a Major League Soccer expansion franchise which began play in 2011 under the name Vancouver Whitecaps FC.

Led by player/head coach Bob Lenarduzzi and his assistant Alan Errington, the 86ers were triumphant in their inaugural CSL match, as they defeated Edmonton Brick Men 4–2 in front of 7,646 fans at Swangard Stadium in Burnaby, BC, on June 7, 1987.

[6][3] The 86ers went on to finish second in the Western Division standings that year before bowing out to inaugural league champions Calgary Kickers in the playoff semifinals.

[3] In 1988–1989, the team, coached by Bob Lenarduzzi, set a North American professional sports record by playing 46 consecutive games without a loss.

[12] In 2001, the team began to use the old Vancouver Whitecaps moniker (signifying both the 'white caps' of the nearby mountains, and the waves of the Pacific Ocean).

[13][14] In 2003, the name was again changed, albeit only slightly, to Whitecaps FC, which encompasses the men's, women's, and youth development teams within the organization.

[15][16] At this time, the Whitecaps logo changed slightly in colour (the light teal-green was replaced with a brighter blue) and the word "Vancouver" was dropped from the image.

The men's team also won the Nation's Cup, a new tournament established by their club as a way to feature the Whitecaps playing against international competition.

The following season, the Whitecaps signed a deal to play an exhibition match against the Los Angeles Galaxy, which featured international David Beckham, and promoted Director of Soccer Operations Bob Lenarduzzi to team president.

[17] In November 2009 the Whitecaps, along with several other teams, announced their intent to leave the USL First Division to become the co-founders of a new North American Soccer League, which was to begin play in 2010.

Following the announcement, MLS commissioner Don Garber commented "there is no doubt the market for professional soccer exists in Vancouver, as we saw last November when nearly 50,000 fans attended the exhibition match between the Los Angeles Galaxy and the Whitecaps".

There was a fair degree of controversy with regards to this location; a Vancouver council session to debate the issue was extended to four nights to allow public input.

Detractors viewed the proposed stadium as an incongruous addition to nearby historic Gastown that would block waterfront access and promote piecemeal development of the area.

On July 11, 2006, Vancouver City Council voted unanimously to proceed with the stadium project, so long as the Whitecaps could meet certain conditions regarding land use.

The Whitecaps also competed on a yearly basis with the Montreal Impact and Toronto FC for the Voyageurs Cup or Canadian Championship.