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Is it really a theological disagreement? Some disagreements that seem to be theological are really philosophy of ministry or strategy issues. Philosophy of ministry issues are also important, but it's unfair to disagree with your senior pastor's strategy and call it a theological issue. To give a small example, I once served under a senior pastor who was very against guns due to some of his experiences doing inner-city ministry. This affected some of our youth events, because laser tag, paint ball, and even water guns were something he was against. While I disagreed with him, it was only a philosophy of ministry issue, and a small one at that--we simply did not play any games with fake guns. Don't make a strategy issue into a theological issue.
Is it a primary theological issue? "Primary" theological issues are issues that are foundational to our faith in Jesus. Examples include the divinity of Jesus, the reality of his resurrection, and the inerrancy of the Bible. For example, whether or not the six days in Genesis 1 are literal 24-hour periods might be an important issue, but it is not a primary issue. Don't make the mistake of turning every single theological issue into matter of primary importance.
Does it affect the way you teach? Are you able to teach from the Bible according to your conscience without contradicting with your church's stated beliefs or the views of your church's leadership in a major way? If the answer is "yes," then in all likelihood the disagreement is fairly minor. If the answer is "no," then you need to talk about that with your church leadership. There will always be minor theological disagreements among church staff members. Don't make a mountain out of a molehill and leave your church over a minor theological disagreement. (Side note: if there is 100% agreement on everything in your church, then you might belong to a cult.)
Does your church leadership welcome the disagreement? The disagreement might be something that your church leadership is well aware of...and okay with. For instance, I would identify "Pre-Tribulation/Post-Tribulation" as an issue that doesn't require 100% agreement on a church staff. Of course, you might feel differently if it's an issue that you feel very strongly about, but the point is that there are some secondary issues that your staff may have already decided to "agree to disagree" on. It's not that they don't feel those issues are important; it's that they don't feel that disagreement on those issues should keep them to from serving together on a church leadership team. That's a different story than if the theological issue at hand is a part of your church's statement of faith.
Does the theological disagreement make me feel like I can't serve at this church? There may be instances when--in good conscience--you don't feel like you can remain at your church, given the theological disagreement. This is not a decision to be made lightly or without a lot of wise counsel. But if you feel like you need to move on, be 100% honest and transparent with your church leadership, and leave well. Don't go all Martin Luther on your church ("Here I stand; I can do no other") over a secondary issue, but rather pave a road for someone else to take your mantle of leadership. If it really is a secondary theological issue, there is no reason you can't leave well and pray that God would bless your church, even though you don't feel like you can serve there anymore.
Do you have any advice for someone who might discover they have significant theological differences with the church he or she serves at?

