Shaughnessy was coached by Rafael Font de Mora (managed by him since age 13 and coached by him for over 20 years). She is the niece of Dan Shaughnessy, a Boston Globe sports columnist.
Shaughnessy made her debut on the WTA Tour in 1996 at a tournament in Budapest and broke into the top 100 in 1998. In 2000, Shaughnessy won her first WTA singles title at Beijing, defeating Iroda Tulyaganova in the final, and breaking into the top fifty. In her breakout year of 2001, Shaughnessy achieved a career-high singles ranking of #11, won the second singles title of her career at Quebec City, and reached the finals of Hamburg and her home tournament in Scottsdale. She also recorded wins over world number five Conchita Martínez, world number four Monica Seles, and world number two Venus Williams.
In 2002, Shaughnessy began the season by reaching the final of Sydney, and recaptured her career-high #11 ranking. She also reached the quarterfinals or better of four other tournaments that year, with wins over top five players Jelena Dokić and Serena Williams. In 2003, Shaughnessy had another excellent year, featuring the second year end top twenty finish of her career. Shaughnessy captured her third career singles title in Canberra, and also had strong Grand Slam results. She defeated Nuria Llagostera Vives, Ľudmila Cervanová, Klára Koukalová and Elena Bovina to reach her first career Slam quarterfinal at the Australian Open, and she reached the Round of 16 at both the US Open and Australian Open. Shaughnessy also scored an upset over world number two Venus Williams in the Round of 16 of the NASDAQ-100 Open in Miami. In 2004, Shaughnessy produced sub-par results, finishing just inside of the top 40, with only one top five win, over Anastasia Myskina in Dubai. However, in 2004 Shaughnessy produced the best doubles results of her career, winning seven tournaments with partner Nadia Petrova, including the WTA Year End Championships in Los Angeles. This doubles partnership is now over as Petrova is looking for a new partner for 2006.
In 2005, Shaughnessy struggled with injuries and consistency. Her year began with a right leg injury, which forced her to withdraw from the Australian Open doubles competition, and from a tournament in Hyderabad. However, Shaughnessy showed signs of recovery in February, reaching the final of Memphis, defeating Nicole Vaidišová in the semifinals. The match featured Shaughnessy serving 22 aces in her 7–6, 7–6 win. After Memphis, Shaughnessy struggled with back injuries for the duration of the spring, not reaching another semifinal until June at a grass tournament in 's-Hertogenbosch.
By July, Shaughnessy's ranking had dropped so low that she was forced to qualify for the Palo Alto tournament. She qualified, and then surprised number five seed Vera Zvonareva in the first round, before losing to Daniela Hantuchová in the second round. A back injury forced Shaughnessy to withdraw from tournaments in Carlsbad, California and Los Angeles. As a wildcard in New Haven, she defeated number nine seed Nathalie Dechy for the first time in ten attempts, before losing to doubles partner Anna-Lena Grönefeld in the second round. In the opening round of the US Open, Shaughnessy led sixteen-year-old Sesil Karatantcheva 6–3, 5–2 and held two match points, before losing 3–6, 7–5, 7–5.
However, on March 24, 2006, Shaughnessy beat Number 3 seed Justine Henin 7–5, 6–4 in the second round (Henin's 1st round) of the NASDAQ-100 Tournament in Miami. Shaughnessy then won a WTA-level event in Rabat, beating 8th seeded Martina Suchá in three sets, 6–2, 3–6, 6–3. It was her 4th tour title. She became the first American to win a WTA-level title in 2006 as well as the first to reach a WTA final in 2006. Shaughnessy afterwards reached the second round at Istanbul, beating 3rd seeded Anna Chakvetadze in the first round. Then she fell in the first round in the French Open to top seeded and crowd favorite Amélie Mauresmo, 6–4, 6–4.
The next year, she faced the previous year's runner-up, Svetlana Kuznetsova, in the second round of the French Open. Shaughnessy raced into a 5–0 lead in the first set, and in the sixth game held three set points on Svetlana's serve. However, Kuznetsova saved them all, won the game and recovered dramatically to clinch the set on a tie-break, before winning the second set 6–3 for the match.
Shaughnessy currently concentrates on doubles, and regularly partners with fellow American Bethanie Mattek-Sands. The pair made it to the doubles finals of the 2011 Indian Wells Masters, by defeating Alisa Kleybanova & Yan Zi (round 1), Raquel Kops-Jones & Abigail Spears (round 2), Liezel Huber & Nadia Petrova (quarter-finals) and Victoria Azarenka & Maria Kirilenko (semi-finals), but lost to Sania Mirza and Elena Vesnina in the finals.
Her coach had been romantically involved with her since before she turned 18. Their romantic and coaching relationship ended in 2005; however, Shaughnessy re-united with Font De Mora as her coach during the latter part of 2006. Shaughnessy claims she was in an intimate relationship from 2004 to 2005, with Major League Baseball player Roberto Alomar, also claiming that he did not inform her whether or not he was HIV positive, during their relationship. Alomar's former wife's lawyer claims that Alomar paid $4 million in settlements to her and Shaughnessy.