| 23 | Minnesota United FC | #tag:ref|#24: Atlanta United → Colorado Rapids. December 11, 2016: Colorado Rapids acquired a second-round selection in the 2017 SuperDraft in exchange for an international roster slot to be used in the 2017 and 2018 seasons.|group="R2 trade"Round 2 tradesAny player marked with a * is part of the Generation Adidas program.
| Pick # | MLS team | Player | Position | College | PDL or NPSL affiliation | Signed | | 45 | Colorado Rapids |  Round 3 tradesRound 4Any player marked with a * is part of the Generation Adidas program.
| Pick # | MLS team | Player | Position | College | PDL or NPSL affiliation | Signed | | 67 | Minnesota United FC |  Round 4 tradesNotable undrafted playersHomegrown players| Original MLS team | Player | Position | College | Conference | Notes | | Colorado Rapids | Kortne Ford | Defender | Denver | Summit | | | Colorado Rapids | Ricardo Perez | Midfielder | Creighton | Big East | | | Columbus Crew | Alex Crognale | Defender | Maryland | Big Ten | | | D.C. United | Ian Harkes | Midfielder | Wake Forest | ACC | 2016 Hermann Trophy winner | | FC Dallas | Reggie Cannon | Defender | UCLA | Pac-12 | | | New York Red Bulls | Arun Basuljevic | Midfielder | Georgetown | Big East | | | New York Red Bulls | Evan Louro | Goalkeeper | Michigan | Big Ten | | | Real Salt Lake | José Hernández | Midfielder | UCLA | Pac-12 | 2016 Pac-12 Player of the Year | | San Jose Earthquakes | Nick Lima | Defender | California | Pac-12 | | | Seattle Sounders FC | Seyi Adekoya | Forward | UCLA | Pac-12 | | | Seattle Sounders FC | Henry Wingo | Midfielder | Washington | Pac-12 | | | Toronto FC | Sergio Camargo | Midfielder | Syracuse | ACC | |
Players who signed outside of MLS| Player | Position | College | Conference | Team | League | Notes | | Sam Brotherton | Defender | Wisconsin | Big Ten | Sunderland | Premier League | |
SummarySchools with multiple draft selections
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