Novo joined Raith Rovers from SD Huesca in July 2001. He made a scoring debut against Airdrieonians on 4 August, and netted the winner during a Challenge Cup match against Alloa Athletic three days later. Novo saw himself sent off in only his third match for Raith, whilst playing against Partick Thistle.

His goal scoring record attracted the attention of Scottish Premier League club Dundee who signed him for £100,000 in July 2002. He made his Scottish Premier League debut on 3 August 2002 in a 1–1 draw with Hearts. Novo scored his first and second goals for the club against Dunfermline Athletic on 17 August but was sent-off in the dying moments of the match for raising his foot at Pars defender Scott Wilson. He went on to score a further seven goals to end the season with a tally of nine.

Novo signed for Rangers on 6 July 2004 for a reported fee of £450,000. He was allocated the number 10 shirt that had been vacated by Michael Mols. In his first season at the club he scored 25 goals, including the goal against Hibernian that won Rangers the league title. He made his debut for Rangers in a Scottish Premier League match away to Aberdeen on 7 August 2004. His first goal came in his second appearance, netting in Rangers’ 2–1 loss to Russian side CSKA Moscow on 10 August.

Novo met Donna Clark in 2004 when playing in Scotland, and the couple were engaged a year later. During a lengthy engagement, they had a son together, Javier, before finally marrying in February 2015 where Novo’s ex-Rangers team-mate, Marvin Andrews, acted as pastor.

With the departure of Alex McLeish and the arrival of Frenchman Paul Le Guen, Novo looked set to leave Rangers. However, a proposed transfer to English First Division club Coventry City fell through on transfer deadline day. Novo initially found his appearances sporadic, featuring in the first game of the season then waiting seven weeks for his second but after a mixture of poor results, injuries and his good performances for the reserves Novo returned to the first team. His first goal of that season, and in over a year, was during a 3–2 UEFA Cup win over Livorno on 19 October 2006. The following match, Novo came off the bench to score a late winner against St Mirren in a 3–2 win. He then started the next game, Motherwell held Rangers to a 1–1 draw with Novo named Man of the Match. His rejuvenated form continued with goals against Heart of Midlothian, Maccabi Haifa and AJ Auxerre. Novo continued to be a regular when Le Guen was replaced with Walter Smith.

The signings of strikers in the summer of 2007 led to increased competition for attacking positions and most of Novo’s appearances in the early months of the season were as a substitute. On 20 October, he started the first Old Firm derby match of the season and scored twice in a 3–0 victory for Rangers over Celtic. On 2 December 2007, it was reported that Rangers were willing to offer Novo a one-year extension to his current contract, which was to expire in July 2008. However, Novo said that he would leave the club if he was not offered a longer contract. He was later offered a two-year contract extension until the summer of 2010, and signed the deal on 21 December 2007.

On 1 May 2008, he scored the winning penalty in the semi final shoot-out against Fiorentina which put Rangers through to the 2008 UEFA Cup Final. During the 2007–08 season Novo was sent off twice, both in league games before cup finals, meaning that he missed both the 2008 League Cup final and the 2008 Scottish Cup final through suspension.

Novo was never selected for the Spanish national team but has played for Galicia – his debut was in a 2008 friendly against Iran, arriving in his homeland just an hour before the match started after playing for Rangers against Celtic earlier in the day. He scored two goals and left to the acclaim of the Galician fans.

On 24 October 2008, it was reported that Novo could be selected by the Scottish national team as he was eligible to acquire a British passport, having lived in Scotland for eight years. This led to much debate amongst the Scottish media as to whether Novo, who was born in Spain and has no Scottish parents or grandparents, should be selected by Scotland. It eventually became clear, however, that the Home Nations would continue to honour a deal whereby that any player selected by England, Northern Ireland, Scotland or Wales would be required to have a blood tie to that country, or have had five years compulsory education within it. This deal would rule out the prospect of Novo playing for Scotland.

The 2008–09 season saw Novo used almost exclusively as a substitute. He came off the bench in the 2009 Scottish Cup Final to score the winning goal after only being on the field for 28 seconds.

In May 2010, Novo moved to La Liga side Sporting de Gijón, on a two-year deal. After a difficult first season in Spain, Novo was offered to clubs in the summer of 2011 with a return to Scotland being mooted. Aberdeen boss Craig Brown said that he had turned down the chance to sign Novo, but this was later denied by the player’s agent.

On 16 February 2012, Novo signed a 6-month contract with Legia Warsaw. He made his debut on 26 February against Śląsk Wrocław and was substituted in the 59th minute with his side leading 3–0, Legia eventually winning 4–0. Novo made 11 League and 3 Cup appearances for Legia, scoring once in a 2–1 win over Arka Gdynia in the semi-final of the Polish Cup.

In July 2012 Novo returned to Spain to rejoin Second division side Huesca with whom he spent a successful 2-year spell between 1999 and 2001. Novo’s second spell at the club was less successful than his first, scoring only 6 league goals. In November 2012, Novo was sent off after scoring in a 2–1 win over Guadalajara for gestures made towards the crowd. Novo protested his innocence, stating that the ‘gestures’ were in fact a “dedication” towards his late mother. Huesca ended being relegated at the end of the season, and Novo became a free agent.

Novo signed a short-term contract with Scottish Championship club Greenock Morton in October 2013, in a deal that was scheduled to run until 12 January 2014. However, after a disappointing return of only one goal, and with Morton at the bottom of the Championship, Novo was released from his contract ahead of schedule on 24 December.

On 30 March 2014 Novo was inducted into the Rangers Hall of Fame along with Fernando Ricksen and Lee McCulloch

On 11 February 2014, Novo signed a short-term deal until the end of the 2013–14 season with Football League One side Carlisle United. He was released in May following their relegation, after appearing in only six matches.

On 11 September 2014, Novo signed for Carolina RailHawks of USL Pro.

On 26 July 2016, it was announced Novo would join Northern Ireland Football League team Glentoran. A few weeks after his arrival in Belfast, Novo was warned by police that he was under a death threat from dissident republicans. The latter part of his season was marred by a six-game ban for a headbutt against Crusaders in January. After scoring a total of 4 goals in 28 games, he was released in May 2017.

In January 2018, 38-year-old Novo suffered a heart attack while playing for a team of Rangers legends at the AOK Masters in Berlin. He was immediately rushed to hospital and underwent emergency surgery.

In August 2018, while at Belfast International Airport to give awards at a children’s football club, Novo was threatened by a Celtic fan.