Connaughton previously played for the Notre Dame Fighting Irish baseball and men's basketball teams. He was selected by the Orioles in the fourth round of the 2014 MLB Draft. The Brooklyn Nets selected him in the second round of the 2015 NBA Draft and traded him to the Portland Trail Blazers.
Connaughton attended St. John's Preparatory School in Danvers, Massachusetts, where he starred in three sports, playing quarterback in football and multiple positions in both baseball and basketball. He received major interest in baseball from schools in the National Collegiate Athletic Association (NCAA) Division I, with Boston College (BC), the University of Virginia, and his original first choice, the University of North Carolina at Chapel Hill, who all made him scholarship offers.
Connaughton's sporting trajectory changed during the summer between his junior and senior years. At that time, he had only received a basketball offer from home-state Bentley University, in NCAA's Division II. He suddenly emerged as a major basketball prospect after what ESPN.com writer Jeff Goodman called "one spectacular week" at the Amateur Athletic Union national tournament in Orlando, Florida, including a game where he had 33 points and 20 rebounds. Connaughton himself would later say, "That week completely changed my entire life." He then began receiving multiple offers in basketball as well as baseball, with many schools willing to let him play both sports. He eventually chose the University of Notre Dame over BC, the University of Miami, the University of California, Los Angeles, and Vanderbilt University.
In 2011, Connaughton's senior year, he was named the Gatorade Massachusetts Boys Basketball Player of the Year. As a pitcher for the baseball team, he had a 11–2 win–loss record with a 1.75 earned run average (ERA) and 160 strikeouts in 90 innings pitched as a senior. According to the baseball scouting site Perfect Game, Connaughton was rated as the 33rd-best player in that year's Major League Baseball (MLB) draft, but he fell to the 38th round, where he was selected by the San Diego Padres, when he made it clear he planned to attend college. He followed through on his commitment to Notre Dame, choosing not to sign with the Padres.
At Notre Dame, Connaughton joined the Notre Dame Fighting Irish as a member of their college baseball and college basketball teams. In his freshman year for the basketball team, Connaughton was one of three players to appear in all of Notre Dame's 34 games. He averaged 7.0 points per game (PPG), 4.4 rebounds per game, and 0.9 assists per game while playing 24.1 minutes per game. The Fighting Irish appeared in the 2012 NCAA Men's Division I Basketball Tournament, but lost to Xavier University in the second round. Connaughton scored 10 points with two assists and two rebounds in 34 minutes of play during the loss. He then joined the baseball team as a relief pitcher.
As a sophomore, in 2013, Connaughton averaged 8.9 PPG for the basketball team, and had a 1.71 ERA for the baseball team. In the summer of 2013, he pitched in collegiate summer baseball for the Harwich Mariners of the Cape Cod Baseball League. In his junior year, he averaged 13.8 PPG for the basketball team and had a 3.92 ERA in ten games started, which included two complete games, for the baseball team.
After his junior year, he was forthright about his intent to return to Notre Dame for his senior basketball season, despite warnings that it would impact his prospects for the upcoming baseball draft. He was drafted by the Baltimore Orioles of Major League Baseball (MLB) in the fourth round, with the 121st overall selection, of the 2014 MLB Draft. One high-ranking MLB executive believed that Connaughton would have been drafted in the first two rounds had he not been committed to returning to Notre Dame for his senior basketball season, telling Goodman, "He definitely cost himself some money," as he expected Connaughton could have earned $1 million if he was willing to quit basketball. He agreed to terms with the Orioles, receiving a signing bonus of over $400,000, with the Orioles permitting Connaughton to play basketball for the Irish in his senior year.
As a senior, Notre Dame's basketball team won its first Atlantic Coast Conference (ACC) championship. He took part in a 2015 tournament game against Kentucky for a Final Four berth, narrowly lost by his team after having sustained a prolonged lead until the six-second mark. Connaughton was determined to finish his degree at Notre Dame, and had a 3.0 grade point average with the university's Mendoza College of Business. He ultimately graduated from Notre Dame in spring 2015.
Connaughton made his professional baseball debut with the Aberdeen IronBirds of the Class A-Short Season New York–Penn League, in which he registered a 96 miles per hour (154 km/h) fastball. At the end of July 2014, he left the IronBirds to return to the Fighting Irish basketball team. Even though the Orioles allowed him to pursue a NBA career, they never made any attempts to recoup the $428,000 signing bonus. As a result, the ballclub will continue to control his contractual baseball rights through 2020, which can be extended for six additional years if the Orioles place him on its major league roster.
Connaughton was drafted with the 41st pick by the Brooklyn Nets in the 2015 NBA draft. His draft rights, along with Mason Plumlee, were then traded to the Portland Trail Blazers for Steve Blake and the draft rights to the 23rd pick in the draft, Rondae Hollis-Jefferson. He signed a three-year deal with the Trail Blazers on July 9. The first two years of the contract are guaranteed, with the stipulation that Connaughton not play professional baseball during that timespan. He made his debut for the Trail Blazers on October 30, 2015, scoring five points in a loss to the Phoenix Suns. He appeared in 34 games for the Trail Blazers as a rookie.
On April 13, 2017, in the Blazers' 2016–17 season finale, Connaughton scored a career-high 19 points in a 103–100 loss to the New Orleans Pelicans.
In Goodman's 2015 story on Connaughton and his decision between two sports, many key individuals in his life testified to his character. His father Len noted, "Patrick is of high moral character and wasn't going to lie to people. That eliminated a bunch of [MLB] teams from taking him at all." Notre Dame head basketball coach Mike Brey added, "In my 15 years here, no one has been more responsible than Pat Connaughton. He's an unbelievable ambassador for us and has shown tremendous loyalty." Family adviser Sam Samardzija, father of current San Francisco Giants pitcher and former Notre Dame baseball and football star Jeff Samardzija, said about Connaughton, "He's not common—kind of like Jeff and [NFL quarterback] Russell Wilson. Not a lot of guys like him come around. He's just wired differently."
Connaughton only allowed himself one luxury with his signing bonus, buying a new Jeep Wrangler. He told Goodman, "The signing bonus is a ton of money, especially for a 21-year-old. But I'm not going to live off that money. At some point, I'm going to live off a college degree." His cousin, Charlie Eckhardt is a star junior basketball player who has faced off with the likes of LeBron James Jr.